Factory 5sp on a 96? I am impressed!
Sure its the tranny?
Not a U joint or other bearing noise that might kick in at higher speeds? Check for the whine when coasting or when accelerating. If on acceleration only, it could be a joint..........sound has a funny way to travelling
If the tranny just came out....check around for loose bolts on drive shaft...and others. I had to use "lock tite" on mine.
I would jack it up and start shaking and spinning things for loose stuff or rotary noises.
I always start at the rear wheel bearings , drive shaft and go forward....I would even check the front bearings.....its that traveling sound thing again
Was the fliud low or is it leaking? I know the 94s Maxda 5spd can develop leaks at "the freeze out type" plugs behind the shift. There is also some stuff out there about a common shifter bushing problems (at top of shifter) 96 may be different.
Go for the simple stuff first.
Good luck .....You'll find it