How Is it to get in bits do you need the top off and then will it all come out backwards?When you disconnect the cable, can you move the lever on the side of the PTO gearbox so that it "feels" like it's engaging better?
It's likely to be either the selector fork, or if it's frequently not been properly engaged when changing between 540/1000 causing the gears to grind, it could be the teeth.
When it jumps out of gear, the selector fork should move the lever on the side that the cable from the cab connects to. If it doesn't, it's most likely the fork.
It's not likely to be shaft bearings since there's no problem with 1000.