P0753 CODE:1999 Jeep GC body-2003 Jeep GC drivetrain

Question

Hey there. I have a 1999 grand Cherokee Laredo 4.0 that I recently replaced the engine, transmission and transfer case out of a 2003 grand Cherokee. Originally, my trans temp over and OD off lights were on from the moment the new drivetrain was installed. Replaced the gov pressure switch and OD solenoid along with the output speed sensor and now I am receiving a P0753 code. My question is do I need to flash my pcm to the 2003 software? I am stuck in limp mode and only have use of gears 2 and 3. I have noticed a wiring difference on the tranny wiring harness to the pcm module plug. I went to my local dealership and was printed out specs for both 1999 and 2003. On the C2 pcm harness for the 1999 and 2003 the 3-4 shift solenoid control are in CAVITY #21. For the CIRCUIT LOCATION, the 1999 is labeled "T121 18BR/WT and the 2003 is labeled "T60 18BR. I need to obviously be looking at these wire locations in particular. How should I go about finding a solution to my problem. Thank you for your time. Andrew