I wouldn't rule out a bad clutch/flywheel or even bad install. The manual transmissions are usually pretty solid.
All of the symptoms sound like what would happen if you tried to force the car into a gear without depressing the clutch fully. An easy test would be test driving on a rack or with the rear wheels off the ground. See if you can now shift the car normally and if the wheels spin with the car in gear, clutch depressed.