Russ, the PTO is engaged with hydraulic pressure. It is not electrical in any way. You should be able to see the linkage going to valve located on the running gear below the operator platform and seat. The seat can be removed and a port in the operator platform allows you to get to the PTO control valve. Normally, when the PTO is lever is placed in OFF, hydraulic pressure is removed from the PTO clutch and the clutch opens to disengage the PTO.
By engaging the PTO at high engine speed, you may have damaged the PTO clutch/brake. If I were you, I'd try to use the rotary cutter with the PTO disengaged. If the cutter slips, that's an indication that the PTO may be trying to disengage and needs to be adjusted. If the PTO does not slip and works just like it is engaged, then you may need a major adjustment or repair of the clutch/brake. The 3PH leaking down is also something that sounds suspicious. I don't think it's possible for the PTO to have any effect on the 3PH, so that sounds like a separate problem.
I think your operator platform will have to be removed and the 3PH assy removed from the tractor to complete a seal repair. The rear transmission housing has to be removed for PTO r&r, so it could end up being a major repair if required. Combined with a 3PH repair, your cost could be pretty high. /forums/images/graemlins/frown.gif