Did you run a re-learn on the new transmission? The TCM adjust solenoid timing based how you drive and the transmission characteristics, new transmission means new characteristics. I would also check the wiring harness to the transmission make sure its connected up good and not damaged.I have a 2005 2500hd 6.6L duramax with a 5 speed allison. When starting the truck up, I noticed there was no light under PRND321 showing what gear I was in. When I backed out of the driveway, the truck rocked backwards and I knew something was off. Before I got out of the neighborhood, the ABS and emergency brake lights came on with a "service brake system" message. The truck wouldn't get out of first, but it did eventually get into second. When coming to a red light, downshifting caused the "range shift inhibited" message to come on, and I had to pull over to turn the truck off. When I turned the truck back on, I was able to move again but continued having the same issues.
When I got it back home, I scanned it and I have 9 error codes appear. The codes were P0404, P0401, P0670, P0700, P0802, U0101, U1000, U1024, U1009. The 404 and 401 codes have to do with EGR, which I plan on deleting at some point but I don't think it is the main issue. The 670 is for the glow plug module control circuit, and the 700 and 802 are a general trans code and a malfunction in the TCM. All the U codes have to do with lost communication with the TCM I believe.
I'm thinking it is a faulty TCM, but I wanted to know if anyone has any other ideas of what it might be before I order a $500 TCM. I took it to a transmission shop and they gave it back to me saying they didn't know what was wrong with it. Also, is it complicated to reprogram the new TCM?