If it's a later 1990 the replacement engine is called an M50 engine. They do swap over with M20's, and I'm not aware of any differences in the manual gearboxes for either engine (if it's a manual). You will need the engine bay wiring loom and ECU too to run the M50, and your battery tray can stay in the engine bay too, there is enough space, just you'll need to fiddle with the wiring a little bit. If your car hasn't got aircon then just strip the pump etc off the M50 engine before you drop it in. You could put the M50 engine & 'box into the car as a complete assembly if you're feeling adventurous!

HTH,

Shaun M