G'Day Mark, well while my last remaining microns of logic suggest that the old Mr Baker is offering the most sensible ignition test, I believe that you have succumbed to "Pommy Ignition Systems Shutdown", or PISS for short. Now I realise that being a brit it's convenient for you to use your home-grown product, but lets face it mate, the Brits (apart from being abysmal sportsmen) were totally incompetent when it came to the black art of auto electrics, as any ex-british bike or car owner will attest.
To further compound the problem, you've added your best efforts with your home made wiring loom, so you don't even have a reliable starting point? My suggestion, for what it's worth, is to take that english paper weight back to M&P and swap it for a Dyna S, then find a Jap to build you a new harness mate, they might have a few disgusting habits like eating raw fish and killing whales for "scientific purposes" that always seem to end up in restaurants, but they're bloody good with wiring, it must have something to do with their little yellow hands, and the fact that they concentrate much better than we do, because they haven't got any friends to distract them with offers of trips to the pub etc.
If you need any more usefull technical advice, you better ask old Mr Baker before he falls off the perch, he's probably got more experience of diabolical electrics in his 60+ years of riding bikes in Britain than anyone, he's a legend! Cheers, Terry.