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There’s 4 different wiring harnesses underneath dash, the main wiring harness is the same between A/T, & M/T. The PCM sub harness, and the drivers control sub harness are different.
VTEC academy has a write up on converting an RSX to manual, YouTube videos as well on how to modify those two harnesses. Otherwise it’s about $300 for the harnesses new from Honda which is what I did, and I just swapped them.
Basically there’s switches on the A/T shifter that you’ll cut out of the harness and extend the wires to the clutch pedal switches.
I bought the correct harnesses from Honda, and swapped them - correct based on year, trim level, body style (coupe vs sedan)

you’ll need an ECU from a matching year. The o2 sensors are different from ‘01-‘03 EX, LX to ‘04-‘05 EX, LX, DX. The ECU has to be a M/T, and match your year.

gauge cluster doesn’t matter. If you swap harnesses instead of modyifing the A/T harnesses. You’ll also need an under dash fuse box from the matching year, trim, body style Civic as your current, but, from a M/T Civic.

really, it’s not worth it, but, I did it with a k pro instead of a stock ECU.
 
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