The lighting circuit has it's own fuse. I believe its 10A. If the fuse checks out, then its a wiring/connection issue, or bad key switch. The PTO utilizes the seat and reverse switches to cut off if the driver isn't seated or the tractor is placed in reverse. To test the circuit, temporarily jumper the switch leads to rule them out. Check all connections. Ultimately, the coil in the PTO could be open.
If you had a bad regulator, your battery would go dead often. When the engine is running the ammeter should show some charging activity. Verify battery voltage of 14 volts or a little more when running at full throttle.