Bike won’t idle with side stand down

I’ve tried to find an exact match to my problem and it’s had me stumped for a while. Bike is a 2006 FZ1. For background scroll to the bottom. The short story is the only thing I can’t do is start the bike to warm up with the stand down

After installing a new Neutral Switch:

Bike will start with side stand down & clutch pulled in

Bike will start in Neutral with the stand up and clutch released

Bike will turn over but not start or run with side stand down in neutral with clutch released

The bike was stolen and recovered a while ago and they cut the ignition and managed to short out the neutral switch. I replaced that and rewired the ignition (I think properly). I’ve been riding it like this for at least a year, it’s just inconvenient because I can’t let it idle unless I’m sitting on it
 
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In the R1/R6 the diode relay controls the dash neutral indicator and makes the decision about the sidestand and clutch interlocks.. I haven't looked at the FZ1 schematic to that detail, but I'd see if there is a diode relay. When they go bad you can get all sorts of weird outcomes, like dull neutral switch when in gear, dash start-up sequence messed up, and of course, weird interlock behaviour.

Sounds like there's a loom fault or a problem with the diode relay.
 
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