I had my TF999 rebuilt 2 years ago. The tranny shop charged me $385 for the rebuild. That was with me pulling the tranny and dropping it off. That included a new torque converter. I will say that my tranny was actually shifting fine when I pulled it. The reason I had it rebuilt was that it was puking fluid when parked. This was also from a reputable shop that I had been dealing with for about 10 years.
1990 Jeep YJ 4.2
Howell EFI, BDS 3.5" lift, M.O.R.E 5/8" Boomerang shackles, 1" Daystar BL, 1" JKS MML, TFI, Crager soft 8s w 35" Dunlop Mud Rovers, Ford 8.8, 4.88s, Dana 30 E-Locker, Terra Flex SYE, Tom Woods CV shaft, Warn M8000.