Why won't my 98 Mitsubishi Diamante shift when hot?

Ok, its a long story, but last fall I bought a 2002 diamante for body parts for my personal 2002 Diamante VR-X. The parts car had a good engine and transmission and ran, drove, and shifted perfectly so I looked around for a car that might need an engine. I found a 98 Diamante for a few hundred bucks that had been run without oil and needed a new engine. I knew my spare engine would work so I bought it. I swapped both the engine and transmission together as one, because the 2002 had 100,000 miles less on it. The transmissions were identical in appearance and were both marked F4A51, so I didn't believe there would be any issues. The engine ran fine after the swap there were no issues there, but the first time I took the car for a test drive, I found that as soon as the transmission began to heat up the car began to shift very hard then quickly went into "limp-home" mode and the green neutral light on the dash began blinking. This would happen every time, the car would shift fine for the first couple minuets that it was cool. I Asked around on some Mitsubishi forums and some Mitsubishi "savy" folks assured me that there gear ratio, and electronic changes in 2001, and it is impossible to swap these transmissions and this was the source of my problems. So unable to find a solution I decided to look at putting the original tranny back in the car to atleast make it drivable. I separated it from the old engine and found that it had very recently been rebuilt, and this made me feel alot better about using it in the car. I swapped the transmissions and made sure everything related to the transmission was exactly as it was originally. The confusing part is that There is NO change in the behavior of the car. It still does the exact same thing. I'm guessing the next thing to blame is the TCU, but would the computer have temperature related problems like that? Anyone have any thoughts?