Steve, I'd love to be able to be there and troubleshoot your tractor, but since that's not gonna happen, here's some suggestions:
The PTO light on while the lever is disengaged is a sure sign that Fuse #2 is blown. Was that the fuse you changed? I'm sure it was. Even so, I'd check all the fuses. There is a replacement self-resetting circuit breaker you can substitute for the fuse and it will make troubleshooting much easier. I don't have the number handy, but an internet search should turn it up.
On tractors that are older, an older battery can cause this fuse to blow. This circuit is right at the peak amount of fused protection and since a lower voltage out of the battery means more current draw...Bingo!...fuse gone. Several people including me have had that problem. I don't think that's your only problem, but it sounds like you now have two problems going at the same time that may or may not be related.
Also, there is a good chance that your ignition switch is bad. Many people have had ignition switches go bad on these tractors. I suspect it's due to moisture freezing inside the switch, but I'm not sure.
Finally, you said you jumpered the PTO relay 1-2 and 3-4. 1-2 is the coil of the relay and that should have blown a fuse if shorted. 3-4 goes to the PTO light on the dash. Are you sure you jumpered the PTO relay, or did you mean to say you jumpered those contacts on the PTO
switch? Emergency brake switch?
I think you may have faulty contacts in your PTO switch or emergency brake switch and also had the fuse 2 problem crop up at the same time. This is a job for an ohm meter to do circuit testing for grounds and opens and switch closures. It's tedious, but necessary. Trying to troubleshoot live circuits may just lead to more blown fuses. Eventually though, you may have to have things powered up or have some hot jumpers to check all the relays. Since you swapped the relays, I have doubt that a relay is problem. The socket might not be making good contact though and your jumper made better contact than the relay itself.
See what I mean about wishing I was there to watch/help? I always have lots more questions than answers.
