I'd suggest a 92-95 EX auto (95 probably being the best choice, but whatever has lowest milage).

ex's have better gear ratio's than lx's. well, they're shorter, anyways.

if gas milage is a big issue, then go with the lx tranny. Also, a stock EX airbox should bolt right up if you install the engine correctly.

axles should be fine, but you might need an EX ecu. Not too sure on that one, tho...

a better place to look for a tranny might be a reputable tranny rebuilding shop...

also, its suggested to change the water pump and timing belt while they're easily accessable (ie, engine is out of car)