When you installed the new flywheel, did you install the pilot bearing for the tranny's input shaft in the center of the flywheel?
(no pilot bearing = no support the tranny's input shaft and the weight of the clutch would make the input shaft whip around causing all kinds of problems)

What did the fingers on the pressure plate look like once it was torqued down to spec? (basically, flat and even = good)

Did you replace the throwout bearing? (just a good thing to replace while you have the tranny out anyway)

I didn't change my '91 CRX Si very much:
-everything is stock except stage1 pressure plate & clutch, blue tokico shocks, and a Mishimoto Radiator (full size dual layer)
-keep daily drivers close to stock for flywheel and clutch/pressure plate is my way of looking at things