Did you remove a pivot bolt about halfway down the driver's side of the transmission? It's there to retain the shift linkage that moves the big bull gear for Granny gear. If the linkage falls off that pivot bolt, there will be definite shifting issues. Pull the top cover off the transmission, and make sure all the shifting forks are engaged in the proper slots in the synchronizers. Reposition the bull gear shifter if it's out of place. Unless the gears are grinding as you try to move the shifter with the clutch depressed, you don't have a problem with your new clutch.
Jerry