As you have seen from the wiring diagram there are 2 relays in the starter Cut out relay box and both are powered buy the kill switch.
Engine turning over rules out the starting circuit and the kill switch.
Check the fuel pump relay by switching on the ignition and turn on the kill switch disconnect the connector to the fuel pump and you should have battery voltage on the red/blue wire. Check the power also on the Red/Blue wire at the injectors and the ECU as this relay supplies power to all these on the red/blue wire.
If you have full battery voltage (might be a volt less) this rules out the Starter cut out relay.
Switching the kill switch to off cuts power to the starter circuit, fuel pump, injectors and ECU.
If all of the above is ok then it is pointing to a dodgy ECU.
It is possible that the faulty earth you had on the black/white wires could have damaged the ECU by the internal circuitry trying to find an earth though a different circuit.
You would have probably seen this often on cars with bad earths and brake light flashing with indicators. Whereas it does not do any harm in that case, in electronic circuits it can be detrimental.
If you are satisfied all the earths to the ECU are intact (vital) and the Starter cut relay is working then I would be looking for a replacement ECU or trying your ECU on another Bike.