Problem with my John Deere 4100?

The battery charging light came on, on my 4100. After a while it went out. I replaced the bulb. Now when I turn the tractor on, without starting, it does not light up. In addition, I can only start the tractor if I move the pto selector to Rear PTo. If I select Mid or Mid and Rear, I cannot start the tractor. If I unplug the safety switch, under the seat, I can still start the tractor, as long as I have selected Rear PTo.
Could there be a problem with my alternator? Or the PTO selection saftey switch? Or the speed selection safety switch?