Did you replace with actual new parts that match the serial of your tractor , or run the new wiring the best you could? Do you have the schematic?

I replaced the wiring harness and circuit board with used parts. All the connections seemed to be correct, however some of the wires were different colors. Also the PTO wires have not been hooked up yet. Looking at the schematic is seems one of the black wires on the PTO has something to do with the purple wire on the start solenoid. I think I might be getting over my head here.
The major difference on the wire harness is the old harness went up the right side of the battery to the PTO, warning lights and light switch. The new harness goes up the left side of the battery. So I might have a later harness. Thanks for your help.

Typically the purple wire should more interact with the safety line of the crank circuit. I don't have that Schematic on this PC, but this wire can run through the relay and most always through the PTO switch. A quick check on JD parts shows different PTO switches and switch modules. Assuming this is a standard 345, rather than a GX345 etc. One would think if the entire harness and all switches were changed that you would be good to go. Maybe as simple as the proper PTO switch? You could compare part numbers between the 2 serial breaks of the switches and other components.

This post was edited by tomplum on Thu, Nov 13, 14 at 11:44

Found the problem. On the used harness that I bought someone cut off the pto connector down by the clutch. Did not pay attention to this until everything else checked out. I found one of the black wires was hot. Hooked the hot black wire to the other black wire and everything now is normal. Thanks for the help.

Good job. Glad you persevered.