I have never heard of any issues with the tf999(Just that you need to reroute the vent hose for the transmission if you plan on driving in deep water.) For the most part they seem to be a good reliable transmission. I have 149K on mine and it shifts great..
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.