Hows this list looks like for everyone??? For a 01 Civic auto to manual.
Tranny
Shift linkage
shifter assembly
pedal assembly
master cylinder
slave cylinder
clutch, flywheel, pressure plate
clutch line
wiring harness dash
engine harness
axels
subframe

 

It's doubful that you need new axles, but aside from that you're set .

 

I'm not sure about the 01, but on 96-00, you'd also need a new intake manifold, throttle body and IACV sensor.
(You would need new axels, too).