I'm assuming that your shifting problem is that the transmission won't stop turning.

The only thing I can think of is, did you adjust the clutch finger height? It should be in the shop manual. What you do is get some key stock, it tells what size in the book. You place 3 pieces of that on the flywheel, and then put the clutch cover on and bolt it down. This all works alot better laying on a bench than it does on the tractor. The key stock takes the place of the clutch disc so that you can measure the distance from the fingers to the flywheel. If this dimension isn't right, it can keep the clutch from fully releasing. If they aren't the same it can keep it from releasing and also cause uneven engagement and wear.

How much free travel does your clutch pedal have?