Someone asked just this question in March's Honda Tuning, and they layed it out very specifically.... I don't know the technicalities to the full extent myself, so dun correct me on any of this, cuz these aren't my words.

(Verbatim quote from the magazine.)
"I own a 99 civic EX. It has been a great car but it is an automatic. An automatic transmission is great for point A-to-point-B driving car, but I have started ordering parts to make modes. What is involved in changing a car from automatic to manual? I heard I can go to the junkyard and get a 5 speed transmission from another car and that the conversion is not difficult. I am currently deployed overseas, so my resources are limited. Thank You."
Sam Hubbard

(answer from Dru Barrios @ Honda Tuning Magazine)
"Samuel, you are on the right track converting from automatic to manual. Dru Barrios says the conversion, however, is not quite as easy as you've heard. You will need a little more then a five-speed transmission to make it happen. Dru reccomends:

¤ Manual transmission, preferably from a '92-00 Civic Ex/Si, but any any '92-00 tranny should work [obviously that answer will differ for you a bit.]
¤ Flywheel
¤ Clutch
¤ Starter
¤ Manual Pedal Assembly
¤ Clutch Master Cylinder
¤ Clutch Slave Cylinder
¤ Clutch Hydraulic Lines
¤ Manual Transmission Mount
¤ Shit Linkage
¤ Shifter
¤ Shift Boot
¤ Shift Knob
¤ P2K ECU from a '99-00 Civic EX with manual
¤ Intake Manifold from a Civic with manual
¤ IACV and Plug from a Civic with manual
¤ Throttle Body from a Civic with manual
¤ Guage Cluster from a Civic with manual (optional)

On an EG/DC Chassis you would have to relocate the bracket that holds the transmission mount, or get a hasport conversion mount. The good thing for EK owners is that Honda got a little smarter in 1996 and made the brackets indentical for both automatics and manuals. It is the mount itself that is different. All you need to do is get the manual mount and you'll be fine.
The worse part for EK ownersis the idle air control valve. On the D16Y8 the intake manifold on an automatic is different than that of a manual; it appears the manual IACV is a plunger type, whereas the valve on the automatic's manifold is a rotary style.If you use the ECU from a manual you will get and IACV errer code if you do not swap the manifold/IACV plug from from 3 wires to two by cutting the stock plug from the wire harness, splicing the yellow/black wire on the harness to the green/black wire on the plug, and splicing the black/blue wire to te black wire on the plug. The orange wire is unnecessary.
All the rest should be a direct swap. You might want to get rid of your automatic gauge cluster in favor of a manual one, but that isn't necessary."


I know this obviously will differ from your car, given the difference in models. But I don't think it'll be tooooooo far off. I apologize in advance if i'm a moron for posting this, I'm new still, and just trying to help any way I can! Hope I was helpful!