ive done the 91 a1 swap in my 88 hf crx. Its fairly involved but not to rough. i got new shift linkage (hasport), mounts (hasport), used stock wiring harness, new axels, new spindles off a teg with brakes, intake (cai aem), header (dc), catalytic converter (gap between header and cat-back is longer that stock so get a longer cat), new flywheel (highly suggest at least resurfacing the one that is one there if the motor is out), new clutch ( once again if motor is out its an easy change if needed) I think thats it if I missed something its probably listed in my sig. Hope I helped.
oh yeah transmission: use the stock ls if your car is cable or if you can find one use a cable b16 tranny for closer ratio gears. if your hydro then try to get a hydro b16 tranny.