If your 24v heinzmann is like the ones I had, it will have 4 wires coming from the hub. Two big wires are the power in. Two small wires go to your ignition switch wire on the controller.
The small wires have a thermal sensor, so the circuit goes like this, from your battery+ add a second small wire. This goes to one of the small wires to the hub. The other wire to the small hub goes to your small red + wire on the controller. If you like, you can add an ignition switch to that circuit too.
Then when the motor starts to overheat, it will shut itself off.
Drilling to cool motors with gears inside no good. It lets dirt into the gears.
It will be fine on 36v, if you use that temp switch in the motor. If you don't, then you need to put a thermometer into the motor, or onto the axle, so you have some idea when the motor is hot, and when it's getting hot too fast.