be prepared to spend alot on a transmission.
se-r trannies in good shape get around 500$ and sometimes more.

i cant remember if the mount locations are the same or not, if not youll have to re weld the mount brackets on.
youll need the transmission, mounts, flywheel, clutch, pedal assembly, clutch cable, flywheel bolts, shifter, both drive axles.

only thigns im not positive on, is if the mount brackets are different, if the ecu needs to be replaced/reprogrammed, and if the spindles are splined the same.

all in all, i would sell the automatic, and buy a 5 speed car.