Sounds like the shifter arm or the shifter fork or possibly both, are bent. The round cover that the PTO handle is attached to removes fairly easily and once you have it open you should be able to see what is out of alignment. here is a link to the parts diagram of the PTO shifter mechanism so you can see what it's supposed to look like.
Ford 3000 PTO shifter mechanism
Ford 3000 PTO shifter mechanism