Infrequent cutting out and magical recovery

[His Dudeness]

You're definitely on the money Dudeness - I went out for a test run, with a bit of wire wedged in the SS ground on the ECU so I could probe it, died within 200yds, no ground. Engine starts up right away if I short the pin to ground, and then dies again when I remove the short.

After a while it decided to work again, and then died for a while after I dropped the seat back down. Wiggling the wiring around the rear of the tail doesn't seem to have any effect. The immobiliser still makes all its usual beeps and things when it won't start - so its power, ground and switched ignition are still good.

Considering it cut out when I placed the seat down, and it wasn't moving, I'm inclined to believe the fault may be in the immobiliser rather than the ignition switch - some kind of transistor-y thing breaking down, as it allows a small amount of current to go to ground when the bike is off. Any better ideas before I make a mess of the immobiliser harness to bypass it... and still have the problem?

Nice one That proves that the fault is the switched ground not getting back to the ignitor. Next you have to find where the open is. I'd start at the ignition since it's the easiest place to test. If you follow the wires off the back of the ignition they go to the junction box under the tank. There are two connectors coming off the ignition, a two pin and a four pin. You're interested in the four pin connector. With your meter on DC Volts put the red lead on the battery positive and the black lead on Blue/Yellow in the four pin connector. You should see 12V on the meter when the side stand is up and OL when it's down. Next put the black lead of the meter on the Black wire in the four pin connector and turn the ignition on. You should see 12V on the meter when the ignition is on and the side stand is up and OL when the ignition is off or the side stand is down. That would prove the ground is getting from the side stand through the ignition and that everything is good up to that point so the fault has to be after the ignition.

If you find a fault in the ignition you could jump the Blue/Yellow to the Black with a bit of wire and the bike should start. If the ignition test good and you have ground coming out of it the next place the ground goes is the alarm connector so you would have to identify that Black wire that's coming out of the ignition at the alarm and check that it still has ground when it gets to the alarm. That's easier said than done since all the wires at the alarm connector are black!