what is the process to swap to a 5 speed? Will one out of a 89 CRX work?

 

yes, that will work.
you will need the pedal assembly, transmission, transmission mounts, axles I believe, shift linkage, shifter assembly, engine harness, ecu, flywheel, clutch, flywheel cover, clutch cable

probably easiest to drop the motor, unbolt the transmission, unbolt the torque converter, unbolt the flywheel, bolt on the manual flywheel, clutch, pressure plate, install shift linkages on car, install ecu, run wires for the reverse lights from the shifter console to the engine bay (they will connect to the reverse switch coming off the transmission), hook up the ECU, swap the engine harness (not sure if you need to do it), swap pedal assembly, install clutch cable, hook everything up and install engine and pray it works.

there's tutorials online, no doubt