The auto trans is soooo slow. You'll like the EX trans much better. There's a couple how-to's for rebuilding a trans in the DIY list:
http://civic-eg.com/viewtopic.php?t=1474
Somehow there isn't an auto to manual swap on there but it has been covered many times in posts. Here's a list of parts needed:
D series Tranny
passenger auto to manual conversion mount
rear Tranny mount
Flywheel
Clutch Disc
Pressure Plate
MANUAL flywheel bolts
Pressure plate bolts
Manual starter
Shift linkage
Shifter
Clutch / brake pedals
Clutch pedal connector (has 2 wires on it that you will be extending later)
Not needed but you can get a standard cluster if you want to have the RPMS and not have the " P R N D4 D3 2 1 "
Center console (its the same as auto but you will need the leather/rubber boot that goes around the shifter)
Manual ECU
Clutch Lines
Master & slave cyls
Clutch fork (engages from slave to clutch)
After you do all the mechanical stuff, there's a little bit of wiring involved so that the reverse lights and the clutch safety switch will work.