Push the clutch all the way in when you shift. I'm guessing by your avatar its a honda.

Model/swap/etc. doesn't really matter. Ones a honda, its all a honda even b series. MOtors change trans are still built the same. (to an extent)

Sounds to me also like a Syncro issue. I doubt, ONE bolt missing will let your trans shift. Hell, i FORGOT to put my rear mount bolt in, because it fell and "out of sight out of mind" took place. Never had any shifting problems.

Good luck, sounds internal.