Turns out it wasnt a crossed wiring harness after all. I inspected the wiring inside of the trans and it is identical to my old stock trans. So from there, I switched out the electronics in the valve body (shift solenoids and TCC solenoid), and got the same problem, ruling out all transmission electronics. Using Darrin's advice, I disconnected the transmission wiring altogether and test drove it again. I got the same problem, but I did NOT get a flashing OD light like you should when the trans wiring is disconnected. This leads us to believe that the ECU itself is bad, most likely from a starter wiring short that I am trying to troubleshoot seperately.
Darrin was nice enough to build me a switch box that I could plug into the transmission and use to manually control the shift solenoids to confirm that the transmission is working correctly. I just got back from the test drive, and the trans shifts very nice when manually controlling the solenoids with the switchbox, runs through all gears, and the torque converter is locking up fine as well.
So, the problem lies in either a bad computer, bad transmission wiring, or both. Since I did not get a flashing OD light with the trans disconnected, I believe the computer itself is definately bad. Anyone have a spare computer with the catch code of NPL2???
As a last note, I would like to thank Darrin for helping me to troubleshoot this fiasco, this car has been a nightmare ever since I got it. He went out of his way to get the switch box put together and shipped out in time to get it to me before the weekend. He has been very patient with me, and has been a tremendous help. I just wish he lived in California