Kawasaki G4TR Trailboss 1 step fwd 2 steps back

This little 100cc Trailboss is still kicking my butt. I had the transmission shifting on the bench before I put it back in the frame, but something has gone amiss. I now can't get it in any positions but neutral and 1st gear. Keeping my fingers crossed that it's shifter related rather than transmission. In other words, I don't really want to split the cases again.