Just my opinion but what I would do is:
-drain fluid in tranny
-remove both back plates and remove the PTO assembly
-fish out the broken pin and any other metal fragments with a magnet
-inspect the shifter clutch for worn splines (as Rick said), check that the set screw is in place and adjusted properly on the shaft (use loctite or stake it to secure the set screw)
-inspect the bronze bushing in the end of the transmission shaft
-inspect the splines on the PTO and transmission shaft
-repair or replace the PTO lever and shaft that is worn
-the bearings sound ok from what you said so you are ahead of the game there.
-button it all back up
Like Rick said, the PTO is very basic, go through and check it out now, repair or replace as needed, and avoid more problems in the future.
Instructions from the service manual via Rudi:http://www.cleancomputes.com/Cub/Blue%2 ... Pulley.htm