Carpenter Questions

When my 06 does that, I put it in gear and rock it back a little. Then put it back in neutral, and the green light usually comes on, and it'll start.
If it was a neutral cut-out issue it should still start in gear with clutch pulled though shouldn't it? That was what I was trying to isolate with my earlier suggestion. Didn't work though
 
If it was a neutral cut-out issue it should still start in gear with clutch pulled though shouldn't it? That was what I was trying to isolate with my earlier suggestion. Didn't work though
I guess if the kickstand is up. I always start mine on the kickstand, and let it warm up a bit. So I've never tried that way.
 
You may have a faulty clutch cutoff switch too.
Try Steele's suggestion first and then if neutral light OK and no success, try jiggling the clutch cut off switch in the clutch perch first and then removing with a small flat blade electrical screwdriver in the release slot where it enters the clutch perch.
Try cycling it manually and/or disconnect and touch wires together to close circuit - which is what happens when clutch lever pulled.
 
I cant get the neutral light to illuminate. But I did try jiggling the clutch switch with no success. Would it not start even if the clutch switch was faulty if it was in neutral?
 
I cant get the neutral light to illuminate. But I did try jiggling the clutch switch with no success. Would it not start even if the clutch switch was faulty if it was in neutral?
Yep, as long as the neutral switch is engaged, and working with the electrical system, ecu etc.
 
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.
 
I cant get the neutral light to illuminate. But I did try jiggling the clutch switch with no success. Would it not start even if the clutch switch was faulty if it was in neutral?
I don't think so. Whether in gear or neutral, the clutch has to be pulled in, or bypassed so the bike thinks it's pulled.