The PTO is working now! Turns out it was the relay. I picked one up last night and stuck it in, but got the same results. I realized this morning that I failed to trip either seat switch.
The way I have wires and switches dangling everywhere, this is a 2 man job. Got my dad to work the seat switches. We tried various combinations and found the BLACK seat switch controls what happens with the PTO. Don't know what the grey one does but it doesn't have any effect on the PTO. To prove it was the relay I put the old one back in, problem was back. Put the new one back on, problem gone again. Hopefully about 15 minutes of tidying up some switches and I should be ready to test mow.