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This is a common problem of ford / lincoln transmissions. Unfortunately the end result usually is a transmission replacement. There is a technical service bulletin for this issue. This is most likely the issue.
Further diagnostics of this code would require a ford specific scan tool
here is a copy of the bulletin
5R555/5R55N/5R55W TRANSMISSIONS - SHIFTCONCERNS, LOSS OF 2ND, 3RD AND 5TH GEAR,INCORRECT RATIO DTC'S - PROCEDURE TOINSPECT AND REPAIR SERVO PIN BORE WEAR
FORD:2002-2005 Thunderbird2005-2009 Mustang2002-2009 Explorer2007-2009 Explorer Sport Trac
LINCOLN:2002-2006 Lincoln LS2003-2005 Aviator
ISSUESome 2002-2009 Explorer, Mountaineer, 2007-2009 Explorer Sport Trac, 2002-2006 Lincoln LS, 2005-2009 Mustang, 2002-2005 Thunderbird and 2003-2005 Aviator vehicles equipped with a 5R55S, 5R55W, and 5R55N transmission may experience shifting concerns. A loss of 2nd, 3rd and 5th gear, may have overdrive band or intermediate band failures due to servo pin case bore wear causing reduced apply pressure.
ACTIONFollow the Service Procedure steps to correct the condition.
For transmissions that have been determined to require an overhaul or rebuild and the overdrive band or intermediate band have excessive wear or burned/damaged band friction material, the cause maybe excessive servo pin case bore wear generally found on higher mileage vehicles, usually accompanied with incorrect ratio diagnostic trouble codes (DTCs), condition becomes worse when hot. (Figure 1)
In our instructions, when we refer to the overdrive bore, we are talking about the smaller bore located closest to the bell housing. When we refer to the intermediate bore, we are talking about the larger bore located next to the line pressure tap.
Inspect and repair the worn-damaged transmission case servo pin bore utilizing the Rotunda Tool 5RW Master Kit part number NRL5RW servo pin bore repair system (1-800-768-8632 option 6).
NOTE DO NOT REAM ABOVE 500 RPM. (Figure 3)
Correctly installed bushings will be flush inside of case. (Figure 9)
The 9/16" and 5/8" reamers require typical maintenance and cleaning of aluminum build up on the cutting edges to help provide optimum bushing installation and increased tool life.
After bushing installation, thoroughly wash the case before rebuilding transmission.
WARRANTY STATUS: Information Only
with it being such a common issue for the service bulletin I wouldn't think it would be.
You could have an issue in the valve body, but i eliminated that since you said you inspected it. Also the valve body pieces usually go bad and not the actual metal body portion - unless it brakes.
if the VSS was at fault it should have tripped a code for the issue, and as long as it is functioning correctly on the speedometer it would further lead me away from it being an issue.
Its hard to diagnose this specific issue without a ford scanner as there are specific test procedures just for this issue.
Hope this helps
Accepts greatly appreciated
Diagram of all solenoids
To ohm the solenoid pack use the diagram i sent above and connect your multimeter to both sides of each wire coming from whichever solenoid you want to check. The current from the multimeter will choose the least path of resistance and activate whichever solenoid you have the wires connected to.
You can reach me back at this same question box. You should still have this on your account as it doesn't time out for 48 hours.