Well I got my 2000 TL back from Acura today. With 87k miles on it they put a new (remanufactured) transmission, fuel regulator, PCM (computer), and front engine mount. I had to pay for the latter. I also had to pay for a new seatbelt that had a bad buckle switch that caused the SRS light to stay on. BTW he told me there was a SB and extended warrantee on the passenger seat sensor and computer for the SRS (but that turned out not to be the problem).
It drives like a new car! The general roughness I was experiencing was obviously the transmission. He claimed the remanufactured transmissions have all new guts. It seems to have extra parts attached to the top compared to the old one so hopefully there were some changes made to the design to fix the problems.