Hmmm. I had the same exact problem with my crx. I replaced the clutch and it did the same thing, i ended up replacing shift linkage, clutch cable, and exchanged the clutch kit itself about three times!
I removed the tranny about 4 times to do all this, and after all was said and done, it was the damn clutch pedal itself!!!!! It seems that most crxs/civic's clutch/brake/accel pedal assembly were made pretty damn poorly. U know that little cylinder that kinda holds the edge of where the clutch pedal pivots(it's like some kind of joint, u can tell by seeing that it is welded to the assembly)? Well on mine, it snapped, and my clutch pedal couldn't get enough leverage to lift the clutch out. I thought everything was okay but apparently that was my problem. Cheap fix too....$25 at a parts yard.
Check the pedal assembly at that joint i'm talking about. If that's not it, then it could be a synchro problem, in that case get another tranny.