PArts needed for the atx-> 5spd swap:

Tranny, you have a choice of stock 3.94 gearing or 3.55 gearing from the neon/pt cruisers. Taller gearing will help with traction for higher hp cars, just make sure you also have a bellhousing setup for the hydraulic clutch as early neons had manual clutches.
Rear tranny mount bracket
Manual ECU (same year as your engine)
Modular clutch and throwout bearing
Bolts from the flywheel to the crank (they are shorter) & from the flywheel to clutch.
Clutch pedal & brake pedal
Clutch master cylinder and slave cylinder
Hydralic lines
Shifter and linkage
Bolts for the shifter
shifter boot


You do not need the axles. The old ones will work.

You will no longer need the TCM.

All the engine sensors remain the same, and you can reuse the wiring harness, at least I did (youll obviously have some unused wiring since your not using any of the tcm stuff).