The final drive gear is the ring and pinion. None of the gears mate with that, so that isn't a concern.
The two shafts that the gears ride on may be different (different diameter, different splines) and that would mean you could not swap. I don't know if they are or not. I do know that you can swap the 5th gear around between D-series transmissions. The 2nd-gen CRX HF will have the tallest 5th gear, though I have read that it isn't a whole lot taller than the 5th from the later Civics. (Something like 0.704 to 0.712 ratio?)
The shop manual for my CRX talked about disassembling and reassembling the transmission. I also used a how-to article from the crxcommunity.com website when I took mine apart and put it back together again. (The input shaft bearing on these seems to die if you leave the oil level low for a long while.)
There is a guy called "Mista Bone" who hangs out on the CRX Community board and more than likely other boards that talk about Civics. He seems to be the D-series transmission guru, although he has some fairly backwards ideas about what makes for good fuel economy...
If your Civic has a B-series engine, I have no idea what will interchange.
-soD
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