That's not a lot of information for us to work with.
1stJDOwner, give us a few more hints. Why did you replace the alternator? Does everything else seem to work ok? Do you engage the PTO with a switch or a mechanical lever?
Did you blow the PTO Fuse?
Next check your seat switch safety...
Next check your Time Delay Control Module...
Next is the PTO magnet Voltage Test...
et cetera...