I've pretty much checked everything I can now and still no joy. The pick-up coils are showing equal Resistance (around 210 ohms) and I have continuity all the way back to the PGM connector. I cant check is the peak voltage from the pick-up coils as I font have the tool for that.
The only thing that is not checking out is the side stand wiring back to the PGM. The G/W wire is supposed to show continuity back to the PGM connector when the side stand is up. The switch itself checks out, as does the warning light. I should be able to start the bike with the side stand down and in neutral though, but no spark still. The G/W wire feels like a red-herring here as that circuit is only complete with the side stand up so surely I should still get a spark with the side-stand down and bike in neutral.
Feeling pretty sure I have a ignition side failure in the PGM.
Any other ideas for me to check?