Have you checked to make sure the master cylinder resevior has enough fluid in it? There may be some leaks in the system. Also, have you checked the master cylinder itself out? It could be getting lazy and not engaging all the way and need to be replaced.
It sounds to me like a problem with the tranny (syncros, etc.) - but if the tranny shifted fine right before you put it in - then it probably isn’t that.
Also, does it make any noise or chattering during normal driving? Did you use a roller pilot bearing or just a solid metal pilot bearing?
It doesn’t seem like it would be a problem with the clutch. If your clutch was having problems - then you should be able to get it to slip by just jamming the gas down hard without shifting.