So, with stand up, gear position is irrelevant. So there are only so many things to check:
Battery - At 12.6 or greater resting volts?
Starter Relay - Could be bad
Headlight Circuit - Common problem on pre-roadster R3s. (No idea if they updated the Touring wiring to match the roadster's, your lights should turn off while cranking if they did).
Clutch Switch - You can try jumping the wire to itself, it's a simple ground loop. This will isolate it as either the problem or not.
ECU - Flash didn't load correctly or an incorrect file was flashed.
Call Bob and explain the problem and steps you've taken, he'll probably want the ECU back to re-flash it.