I recently bought a 99 4x with 5 speed manual I was checking all fluids and transfer case was real low and tranny was a little low I was told to put atf in transfer case and did did not have any synthetic oil for tranny after driving it for a few days I went to put oil in tranny and it was way over full and transfer case was really low again both tranny and transfer are the HD with PTO ???

 

The transfer case must be leaking, it doesn't share oil with the transmission. Were they level when you checked them, or on ramps?

 

I've heard of this the other way around with automatic transmissions which obviously use ATF like the transfer case. I'd loosen the nuts between the TC and transmission and crack it open a bit. If there's ATF coming out the TC input seal needs replaced.