There is a TSB for intermittent OD light flashing with codes 645 or 646 or 647 or 648.
647 as you mention idicates that the PCM has detected loss of third gear.
You will need to follow TSB 98-5-16.
As read below:
CALIBRATION:
5-58B-R10, 5-58R-R10
WARNING: THIS MODIFICATION IS AUTHORIZED ONLY FOR THE LISTED ENGINE. PERFORMING THIS MODIFICATION ON OTHER ENGINE CALIBRATIONS IS UNAUTHORIZED AND COULD CREATE LIABILITY UNDER APPLICABLE FEDERAL OR LOCAL LAWS.
ISSUE:
Some vehicles may experience a flashing “O/D OFF” lamp and/or the following Diagnostic Trouble Codes (DTCs) may occur: 645, 646, 647, 648. This may be caused by a damaged intermediate and/or overdrive servo piston seal, faulty Throttle Position (TP) sensor wiring or a concern with the transmission control strategy.
ACTION:
Follow the diagnostic procedures listed in the 1995 Explorer Service Manual and the following text for details.
Service all non-transmission DTCs and concerns first.
Service all transmission DTCs and concerns except for DTCs 645, 646, 647, 648.
For the above DTCs, follow TSB 97-17-24 making sure that the Electronic Pressure Control (EPC) solenoid is functional, transmission bands are adjusted properly, and the servos are not damaged.
Check the TP sensor wiring, wiring crimps, and peform a wiggle test.
If after checking the transmission and TP wiring no problems were identified, verify the vehicle has the latest level calibration. If it does not, replace the Powertrain Control Module (PCM). Refer to the following PCM Application Chart for correct PCM usage.
PCM APPLICATION
Old Calibration Old Part Number (-12A650-) New Calibration New Part Number (-12A650-)
5-58B-R10 F5TF-ARC 5-58B-R10 F5PF-BRA
5-58R-R10 F5TF-ATC 5-58R-R10 F5PF-BSA
NOTE: Another item to inspect before for you go crazy with PCMs and calibrations… YOu have both bank lean codes… Air fuel ratio calculation is based on MAF reading… If MAF or TP are erratic, engine load calculation will be biased… This load calculation is used for transmission control. Either Line pressure will be high or low depending on system bias. Vehicle is a bit old to suddenly have calibration issues, however PCM failure may be possible.You should rule out the basic PCM inputs and basic driveability issues first. Fuel Pressure? MAF reading at idle and on accel, IAT and TP variability/inconsistency.
You must get the engine performance side back first, then deal with transmission second. Once driveability is cleaned up, then bands and servos should be checked. I would only assume the transmission shop did verify the servo and band integrity. But then again in this business you can’t assume anything.