so i got the transaxles out, thats all good. so i started unbolting the mounts to the transmission, then took the bolts from the transmission to engine out. now i think im done but i cant get the transmission off the engine, please help. idk what to do

 

You need to support the flywheel end of the engine and remove both the right side mount and the back one. Remove all the bolts, there are small ones holding the sheet metal plate on the bottom, and the starter has to come off. The transmission pulls straight away from the engine; it has two alignment pins one front and one back. Ideally use an engine crane to support the weight of the transmission.

 

i have two jacks under the car, along with jackstands and such, the jacks are supporting the oil pan and the transmission. i have all three transmission mounts off completely, and the 5 bolts that hold the engine to the transmission, along with the exhaust header bracket off. i tried jacking and lowering the transmission, and wiggling it around. i think its stuck =( maybe ill go buy an engine hoist?

 

i had to fit a pry bar inbetween the transmission case and the flywheel to start getting it off. honestly, it's almost easier to drop the motor to do this stuff, ha ha. =P
makes you want to get a 5 speed transmission knowing how much work it is to change it now, eh? =P

 

lol if i knew i was getting a new transmission i would just cut holes in it and put a rope or something threw it and pull, im afraid of damaging my transmission which is why im being so careful. but yes i do kinda want a 5-speed. is there any wireing you need to change? or do i just need to find one from a civic/crx si of my generation?

 

The black stuff is clutch dust. It's the same as the brake dust that gets on the front wheels from the brake pads wearing down during normal use. It's not going to hurt anything.

 

no wiring mods needed, just a transmission from your generation.
Civic/CRX Si = best, shortest gears
Civic DX/CRX DX = long gears, but 5 speed
Civic STD/CRX HF = long gears, 4 speed
well, not sure on the HF, but maybe.