The first thing I would do would be to start the engine (outside) and let it idle for about 30 minuts, in order to get everything heated up and dried out. Then take it on a 10-15 mile road trip to exercize the tranny and gears. Then re-assess the situation and see what works and what doesn't.

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.