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Can I get the engine serial number please. As Merc makes a few different style EFI engines. Also, do you have access to a scan tool?
Serial # XXXXX
Model #(NNN) NNN-NNNN
Do not have access to a scan tool
If you brough this to me, here is how I would troubleshoot it.
The very first thing I would do is hook it up to a scan tool/laptop and see if any sensor stood out as being bad. Since you don't have access to a scan tool, your going to only check what you can check without one.
Next I would check the fuel pressure when running and compare it to spec. On yours its 34 to 36 psi. Check it when the engine falls on it's face. If the fuel pressure maintains, then we know the fuel pressure is good, and the rest of the fuel system is likely fine. If it falls on its face, then you need to dig into the fuel system a little deeper.
After that, I would do a compression test on both engines. It always starts with compression, and if the engine has low compression you could end up throwing good money after bad trying to find a problem that is really low compression. On that engine all cylinders should be about 90psi or better, and all within 10-15 of eachother.
Next I would do a spark test.
These are the testers we use in the industry.
But you can also get cheap spark checkers at most good autoparts stores.
You need to hook the spark tool up and set the gap to 7/16ths of an inch. The spark should easily jump that gap, be hot and blue in color, and be consistant with engine rpms. Weak looking yellow spark will not cut it.
Either way, that is how I would do it. Going about it in the order I mentioned above is the most cost effective way to troubleshoot it so that your both not wasting time and not skipping around/making mistakes. Once you know which system is acting up, compression, fuel, and ignition, you can dig deeper into those systems. If all systems pass all of the above tests, then your looking at a fault in the EFI system, and the engine will have to go on the scan tool/laptop to diagniose.
Hopefully that gets you pointed in the right direction, and leads to solving the problem.
Post back with questions
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PS- One thing those engines are known for is getting a clogged VST (vapor seperator tank). Underneath the high pressure pump inside of the VST, is a little filter screen. If the fuel pressure drops, that little screen is highly suspect as to causing the problem, as they clog up often.
It means the filter could be clogged, or there is another restriction in the fuel system some place. There is 1 more test you can do, it's called a boat side fuel system test. It tests for restrictions in the fuel system. I was only going to give it to you if you came back and told me fuel pressure was low. (I didn't want to give you information overload!)
boat side fuel system test -- click here
Now if there is any kind of restriction in the fuel system (which would limit fuel to the engine and cut rpms) that test will find it.
Start by replacing the fuel filter first and trying it. If that doesn't solve it, run the test and see what the fuel system is pulling for vacuum. If you have any questions about the test or the results you get from it, by all means just ask away.