This bike is Pi**ing me off?

I lost my keys so I put on the spare ignition switch I had. (yes you heard me right) Bot keys lost. Now the thing wont start unless I ground out the ground side of the switch. Freaky. Ive got a lack of ground from either the start enable box to the switch or the side stand switch is faulty. the weird thing is is that th switch is good and the other switch did not expose this problem. Also, it wont stay running with the clutch out, even when in neutral if the side stand is down. Think about this for a second. Seems simple to diagnose until you consider the the side stand issue. Oh, i just remembered. the neutral switch is faulty. So that explains that. But, Im not looking for a diagnosis on the internet here, and I want to avoid really tearing into the harness, but I have a strong feeling that ive got a broken ground connection somewhere. Anyone seen or know of any similar common problems with the R1 (99-2001). If the answer is yes, then ill dig into it, but if theres no common knowledge of it, then ill just get another, since i wont have a high chance of the same thing being wrong with a doner. This is just a quirky problem that doesnt seem to make sense. If nothing else, I guess I am letting the frustration out...