I can't speak to the manual tranny... But I've run my TF999 with the AMC 360 V8, Dana 300, 4.56 gears and lockers in both axles, and 35" tires. I haven't done a lot of mudding (hate clean up), but it has been over a few rocks. I have an extra tranny cooler in front of the radiator. Never had a bit of trouble with the TF999.

1977 CJ-7, fiberglass body, AMC 360 w/ headers, DUI ignition, Edelbrock intake and Holley 4150 carb, TF999, Dana 300, 4.56 gears lockers, York air comp, 4" susp lift, 2" body lift, BFG 35" M-T tires, Megashifter, AGR pump & box, REP8000 winch.