4.44 swap tcu

[Indy]

I did the trans swap and after the trans still was stuck in safe mode. It worked for about a block, then failed. I found a guy who would work on it (the dealer told me it was too old and they had end of life it). The mechanic said the trans was a version 3 and the tcu was a version 2. He changed the tcu and moved a couple of pins. The trans works ok until I put my foot in it. Then it shifts at about 5000 rpm and it feels like the engine shuts off for a split second. It decelerates hard, then accelerates again until the next shift. Any ideas on what to do? I haven't had a chance to take it back, but if anyone can shed some light before I do, I would appreciate it. Thank you