Golfwiz07

What's up people, this is my first time posting and I have a question. I purchased a 1997 es300 with a good engine and tranny 60,000 miles ( Whole rear end was totaled) . I wanted to put that complete set up in my 1999 es300 but my mechanic is telling me it will not work cause i have a U140E transmission (18 bolts) in my 99 and the computer won't be able to read the 97 set up. If anyone out there has any ideas please let me know. Thanks.