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Chris (aka- Moose)
Chris (aka- Moose), Technician
Category: Lincoln
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Experience:  16 years experience with Lincoln
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Lincoln LS V6: I need a Lincoln LS V6 expert. My car is a

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I need a Lincoln LS V6 expert. My car is a 2003 Lincoln LS with 3.0L V6 engine and automatic transmission, manufactured January 2003, 150K miles (VIN 1LNHM86S93Y659890). This is the 2nd-generation car with throttle-by-wire and PCV valve on driver's side valve cover. I bought this used car a few months ago and have enjoyed it. Previous owner indicated he had purchased the car used in 2006 and had maintained it well. Until a few weeks ago, it ran great. A few weeks ago, it went into "limp-home" mode without prior warning or other symptoms. When the tow-truck arrived to haul it to my home, it started normally and was able to be driven onto the truck bed. I had it towed anyway out of concern it might fail again (instrument panel showed both the "wrench" symbol and the check-engine light). After I got it home, I drove it and found that it would run 5-6 minutes, then cut off as though there was no ignition; 2-3 minutes later, it would start again and run 5-6 more minutes. I drove it to Autozone and asked them to read codes in the diagnostic system. They found the following. P0446 P0606 P1235 P2107 P2110 Because I know these cars can be sensitive to coils and plugs, I replaced all 6 of each (Motorcraft OEM plugs, gapped correctly, and Hungarian-made Visteon coils). I'm an experienced amateur auto-technician and did the work myself ... didn't find it as difficult as I thought it might be. All the old plugs were OEM Motorcraft and looked like they were burning correctly. Of the six old coils, only four were OEM Motorcraft so I assume at least two had been replaced previously. No evidence of leaks at valve-cover gaskets (no oil in spark plug wells) or intake manifold air valves. I pulled the upper intake manifold but not the lower manifold. I re-used the six oval-shaped upper intake manifold gaskets after careful cleaning and inspection (no gasket sealant, just re-installed them "naked") and torqued everything properly. When I put everything back together and tried to start the car to bleed the cooling system, I found the battery (new Interstate Megatron) almost dead as though something had been draining it. Although the battery barely had enough power to crank the car, it did eventually start. The car seems to have similar problem as before only now it won't run 5-6 mintues ... runs only 60-90 seconds, then dies (but can be re-started immediately). It won't run long enough to allow the cooling system to be bled. Some info I read in an on-line Lincoln forum suggests the problem could be leaking intake gaskets, throttle body, or faulty engine management computer. To rule out the easiest of the 3, I'm buying new upper intake gaskets today from local Lincoln dealer and will install them tonight. I need your advice regarding how to test throttle body and computer, also any other ideas you might have about what the problem might be. Check-engine light is still on but not the wrench light. I haven't been able to drive back to Autozone to get codes read again but would be willing to buy a code scanner and read them myself if you think it would help. Thanks in advance for your help.

Hi, I’m Chris. Welcome and thanks for asking your question!


Sorry you having this trouble, thanks for all the great details. Code 0446 is an EVAP canister vent code, it needs to be addressed later, not now because it is not causing this. Code 0606 means you have a faulty PCM or throttle body. 1235 means you have a fuel pump communication concern. 2107 means you have a throttle body or PCM thats bad or wiring issue to the throttle body. 2110 means the computer has limited the power to prevent the engine racing over speed.


Once you have gotten the car repaired and running correct, or at least gotten the other codes resolved. If the code 0606 comes back then you have to replace the PCM for a internal error.


For code 1235 you must diagnose all throttle body codes before addressing the fuel pump or pump driver module or PCM or wiring.


So lets address 2107 first. Here is what ford says to do.

Normally faulty ignition coils cause this concern, since they have been addressed lets also unplug and disconnect the alternator.


Start with these things and let me know the results so we can continue on.


Customer: replied 4 years ago.

Thanks for your answer. Given your experience, I feel confident you can help me. I read the file you attached but don't know how to follow the instructions in it. I'm familiar with OHM meters and how to check resistance but I'm not familiar with the "pins" the file says need to be checked or the acronyms it references (TACM, ETCREF, DTCS, for example). I know how to unplug and disconnect the alternator. I'll do that in the morning and let you know what happens. I didn't get the upper intake manifold gaskets replaced yet. Do you think that's a priority or should I skip that for now and just unplug the alternator, start it, and see what happens? Also, I disconnected the battery apprx 24hrs ago and removed it from the car to be recharged. I've been told t24hrs without battery power will reset the car's computer and may help in this situation. I'll reconnect the battery in the morning, start the car, and let you know what I find out. Thanks again for your help.

There are only 2 wires going the throttle motor.


When the throttle is opening, one is positive and the other is ground. When the throttle is closing the wire polarity swaps. Pretty much just OHM test the wires from the computer to the throttle body to verify no resistance and verify neither show continuity to power or ground.


TACM=throttle actuator control module processor = a fancy name for the vehicles computer (PCM).

ETCREF/RTN= electronic throttle control reference signal or return.

DTC= Diagnostic trouble codes for example P2107



I would not even worry with the intake gaskets. A car computer resets after 10 minutes of no power.


Customer: replied 4 years ago.

Thanks for the quick reply. I'll do what you suggest in the morning and let you know what happens.

Sounds good Jay, I will be available for the most of today, but a little detained in the evening while the race is on.
Customer: replied 4 years ago.

Good morning. After I disconnected and unplugged the alternator, the car started and ran for several minutes (5-6) before dying again. It re-started after 1-2 minutes but then died again after only 2-3 min. I was running the heater and fan on high at the time in an attempt to finish filling/bleeding the cooling system. I suppose it ran 5-6 min initially because it didn't die until reaching a certain temp but that's only a guess.


I unplugged the wires to the throttle motor and checked their voltage as you suggested. With alternator unplugged and disconnected, key in "on" position but car not started, foot not touching the accelerator pedal, I got 4 volts at each wire. I checked also when pressing/releasing the accelerator pedal and found the voltage didn't vary. Based on your instructions, this isn't what I expected to find.


I haven't yet checked resistance between PCM and the throttle motor terminals because I'm not sure how to to do it. Please advise where the pcm is and which pins to use to check that.

Jay on your car the PCM is near the right front shock tower, see below.


You are going to be checking pins 27 YE/BU and 35 WH/BU.


Lets also check and make sure the ignition transformers are grounded on the block wit ha good clean connection, both are on the backs of the heads, see below.



Customer: replied 4 years ago.

I removed cabin air filter and filter box, exposing the PCM behind the right front shock tower. I disconnected the center plug from the PCM but I don't see anywhere that the pins are numbered so I can't tell which ones are 27 and 35. At the throttle body, I see that the 2 wires are YE/BU and WH/BU but I don't understand how to find the same wires where they plug into the PCM.


Although access seems impossible without removing the motor from the car, I also attempted to check the ignition transformers ... located them on the back of the heads "blindly" by hand from your diagrams and felt around as best I could to make sure the connections seemed tight and free of corrosion (they do). If it's critical, I could attempt to access the connections from under the car to R&R them but it doesn't appear to be much easier. Please advise.

Jay you need to check the wire colors o n the back side of the connector to verify your at the correct pins.


I had a feeling you may not be able to get to the transformers, it has been a while since I tried. So I was unsure if they could be gotten to easy. They are grounded to the block, if you can get to them to sand the contact surfaces down that would be great, but if not we will have to skip that step and move on.


If you have access to a scan tool that can do a key on engine off scan that may also help, to see if anything is setting a code while not running. The coils really confuse the throttle body signals alot and sometimes new ones are even bad, so if we can still get throttle body codes not running then we could rule out the alternator and the coils.


Customer: replied 4 years ago.

Thanks to your diagram, I was able to check the throttle body wires as follows.

(a) Continuity from end of wire where it plugs into PCM to end of wire where it plugs into throttle motor. Yes

(b) Continuity to ground from end of wire where it plugs into PCM to chassis. No

(c) Voltage in wire when battery is connected but ignition switch is off (indicating “short” to live wire somewhere in ignition harness). No

I think this is all the tests you recommended for the throttle body wiring. If not, let me know. All the answers I got seem to indicate the wiring is OK.

I’m about to jack the car up and see if I can R&R the ignition transformers as you suggested so we can rule out faulty ground connection there.

I’ll check into buying the key on engine off scan tool so I can see if there are codes. The check-engine light wasn’t on the last time I started the car but I understand you to be saying there’s a possibility of stored codes anyway.

I’ll get back to you shortly. Thanks so much for your help and quick answers. If you can walk me through solving this problem, I’ll be glad to pay bonus. You seem to know a lot about these cars but I’m depending on your integrity to let me know if you’re in over your head (like I am). If throttle body is the problem, I can do it myself. However, I have a feeling I’m going to end up having to have the car towed to Lincoln dealer for PCM replacement and re-flash. I hope not.

Yes Jay, there can be codes without a light on. Yes the wiring looks good from those tests. So far it is looking like a faulty throttle body, but I and many others have been hundreds of times with wiring or coil or radio interference concerns.


Look at this file below and you can see how very few times the throttle body is to blame. This is a site I pay to have a subscription to help in circumstances like this.



Customer: replied 4 years ago.

Thanks again for your quick answer and the obvious lengths to which you go to make sure you’re giving good answers. Your customer ratings are outstanding and I trust your advice … don’t mean to sound like I don’t … I’m just a wee bit frustrated.

Believe it or not, access to ignition transformers is worse from under the car than from above so I think it’ll be impossible to R&R them as you describe unless I remove the upper intake manifold again. If necessary, I’ll do that … was planning to do it to replace the upper intake gaskets, anyway, until you said you didn’t think it was a priority. Is there a way to establish a temporary external ground to the transformers so I can see if it makes a difference before I go to the trouble of removing the manifold to R&R them?

I’m going to get the scan tool … will get back to you asap.

Thanks Jay, and trust me I can understand your frustration. The LS is one of the least favorite to work on vehicles, since it is based off of a Jaguar, not a Ford.


Since you were going to go ahead and do the gaskets, replacing them sure will not hurt anything and this will at least give us access to the transformers. Since you can not reach, them odds are you can not provide remote ground either, or at least sufficient enough.


We are coming up on late in the day here in TN and my folks are coming to dinner to watch the race with my wife and son and I. So I may not be as quick on replies, but i will see one if you post one.


Customer: replied 4 years ago.

Thanks. Hope you guys enjoy the race. I'll be watching, too, off and on. There are many drivers I like but, overall, I pull mostly for XXXXX XXXXX and Jeff Gordon. The Busch brothers have a lot of talent but they tend to get on my nerves.

XXXXX XXXXX household here. We go to bristol every spring 13 years strong. The Busch boys are strong Bristol. I think is going to be Keslowskis day though. I live about 6 hours west of the track. I hope nascar gets back to fun to watch, but I also hope gas goes down.
Customer: replied 4 years ago.
, ,I got a scanner. The battery has been disconnected most of the day so I figured the computer’s code memory would be blank. I wanted to give it a chance to throw some codes so I connected the battery (alternator still disconnected and unplugged) and started the car, letting it idle for 8 min on battery power. It didn’t die but I turned it off after 8 min. It idled because it wouldn’t do anything else … throttle body was plugged in but there was no response to the accelerator pedal. On the instrument panel, the check-engine light wasn’t on but the “wrench” symbol was. After I turned the engine off, I turned the ignition to the “on” position, plugged the scanner in, and logged the following codes: P2104, P0138, P0708, P0743, P0755, P0765, P2196, P2198. There’s also “freeze frame” data that I can download. Some of these codes seem relate to the transmission and I have no idea why. Although I did put the car in gear at one point while it was idling, I didn’t let it move. It felt normal when I put it in gear.Unless you have a better idea, my next step will be to remove the upper intake manifold and replace the gaskets. The Ford dealer says to install them without gasket sealer. While I have the intake manifold removed, I’ll attempt to R&R the ignition transformer grounds as you’ve described. If you have a better idea, let me know. Otherwise, I’ll be back in touch after I’m finished with the gaskets.

Your car is making things difficult. 2104 means you still have throttle body concerns. 0138, 2196, 2198 are all O2 sensor codes. All the 07 codes are trans concerns. Only the 2104 is associated with the lack of throttle. Al the others will cause running issues. Once thing the trans codes and O2 codes do have in common is fuse #6 which is the power for the EVAP system, you have a prior code for that and it powers the solenoids. This fuse if blown or having an excessive draw can cause air/fuel running issues which sets O2 codes.


I suggest you continue with the intake for now.


Customer: replied 4 years ago.

The Bible says the God gives wisdom to those who ask and I‘m asking. Obviously, I need it. Frown


Tomorrow after church I’ll check fuse #6, change the intake gaskets, re-ground the ignition transformers, re-connect the alternator, and start the car again. Battery is currently disconnected so I suppose existing codes will be erased by the time I start the car again. I’ll let you know what happens. Thanks again for all your help.

Tomorrow once the repair is finished, connect the battery. Turn the key to run, but do not start the car. Now scan it, and see which codes you get. Then start it and scan once again. I will wait to hear from you afternoon tomorrow.


Customer: replied 4 years ago.

10-4. It'll probably be almost dark before I can finish and get back to you.

That will be fine
Customer: replied 4 years ago.

I'm finally finished with everything and I followed your scanner instructions. Don't know if you're still awake, but I'll send you the results tonight ... it'll take a few minutes for me to write up the codes. Short story is the car still only runs 60-90 seconds before dying, wrench symbol and check-engine lights are still lit, there's no response to the accelerator pedal, and there's a cooling fan that runs constantly from the moment the ignition switch is turned to the "on" position. I'm done for tonight and won't be able to work on the car again until tomorrow night, so there's no rush for you to answer. As always, thanks for your help.

I am still up but heading to bed myself very shortly.


Customer: replied 4 years ago.

I followed the plan outlined last night ... changed the intake gaskets, R&R’d both ignition transformers (remove, sandpaper both grounding surfaces, clean surfaces with electronics cleaner, and re-attach), checked #6 fuse in both fuseboxes (trunk and cockpit), and reconnected the alternator, then followed your instructions about scanning codes. I'm done for tonight and won't be able to work on the car again until tomorrow night, so there's no rush for you to answer. Here are the codes.

Initial code reading. Battery had been disconnected for apprx 24 hrs. I put the car back together and re-connected the battery, then turned the ignition to on position (didn’t start the car). Code P2104. I erased the code.

Second code reading. I started the car. It only ran 60-90 seconds before dying, wrench symbol and check-engine lights were lit constantly, there's no response to the accelerator pedal, and there's a cooling fan that runs constantly from the moment the ignition switch is turned to the "on" position. The cooling fan running constantly is new; the car won’t run long enough to get to operating temp but I assume the PCM is sensing that it’s over-heating.

I’m unfamiliar with my new scanner ($100 bucks from Wally World) but it read 12 “generic” codes and 1 Ford-specific code as follows: P2104 P0606 P0708 P0743 P0755 P0765 P1235(Ford) P2107 P2198 P0138 P0750 P2196.

After the generic codes, the scanner asked for car manufacturer and ran a “KOEO Ford/Mazda enhanced test” scan to come up with the following 20 Ford/Mazda codes. P0060 P0121 P0480 P0708 P0713 P0740 P0743 P0748 P0750 P0753 P0755 P0758 P0765 P0768 P0960 P1000 P1702 P2104 P2121 P2122

Hope this info helps. To me, it seems like the car is getting worse instead of better. Let me know what you think the next step is.

Jay it does look like it is getting worse. Since you are still setting codes for the throttle body prior to even starting the car, this means the throttle body has to be bad. You have done all the wire tests for the throttle body which passed, and it is still setting codes even though h the coils nor alternator nor transformers are being used while the car is just i n the RUN position.


The 0606 code has me worried since that is a faulty PCM code, but it can store from other codes being stored.

Let me also get you the description for every code, click HERE and HERE

Customer: replied 4 years ago.

  1. I think I understand you to be saying you think it’s throttle body or PCM, perhaps both, but that I should start with the throttle body. Right?

  2. If throttle body, I assume it’s not repairable but rather just gets replaced. Right? It appears to be a “plug & play” part that I can buy and replace myself … no programming required. Right? Not necessarily a Lincoln OEM part as long as it’s from a reputable manufacturer. Right?

  3. I don’t want to abuse you by riding this $38 question forever. I assume this is a good stopping point and am going to go ahead and rank your answers as excellent. Even though we haven’t yet succeeded in fixing my car, you’ve been very helpful. Thanks!

That is correct, I would start with the throttle body.


The throttle body is not repairable.


It is plug and play, replaced while the battery is disconnected, no programming and can be done at home. I have had no problems using the aftermarket throttle bodies.


I would appreciate a current ranking, and we can still work on this and hopefully get it resolved.


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