Most (maybe all?) Honda engines are NOT different, but thier ECMs are different for auto vs. manual. It depends on what car, what year you're talking about.

Generally you need this stuff...
- Flywheel & clutch from a manual car, along with the longer bolts that hold the flywheel to the crankshaft.
- Clutch pedal & hydraulic system. (or cable for some models/years)
- Console, shift lever, shift linkage or cables. (depends on model & year)
- Wiring for starter interlocks. (clutch switch interlocks starter on manual, shift lever interlocks starter on automatic)
- Maybe instrument cluster? (manual cars don't have PRND321 lamps)
- Maybe ECM/TCM depending on year?

At least you need to think about each of those things. You can probably leave the PRND321 lamps & they simply won't work. Some years you can keep your same ECM.

Still, swapping the tranny is a big job. Try a couple fluid changes first, if it's OK then at least you can sell it as a 'working' tranny. When you drain auto tranny fluid, you only get about 1/3 of it out. So drive 10 miles & change it again. And again... And use real Honda ATF, it seems to make a difference.