Hi Anthony,
If the +5V supply is only 0.1V it could be a faulty 5V regulator chip inside the controller or an external short to ground on one of the +5V wires for the throttle/Hall sensors etc.
Try disconnecting the throttle and unplugging the hall sensors to see if the 5V supply returns. If it does, this may indicate either a short circuit or a weak 5V regulator output.
Reconnect them one at a time to see how each of them affects the voltage on the +5V circuit.
If it is just a fault with the +5V regulator chip, you may be able to get the controller to work again by supplying a 5V supply from an external source.
3x AA batteries in series should work for testing, and these could be replaced by a suitable DC/DC converter for a more permanent fix if the external supply cures the problem.
Alan