I am late to the party on this, but reading through what all has been done and checked, not much left but a couple things.
reading your story, it all pointed to the ignition pickup, I was surprised that changing that did not resolve the problem. However, I have been down that road before and found that my replacement (new) pickup sensor did not work either, it can be checked with the multimeter, values in the manual. I finally threw an old pickup sensor off a running bike on there and it fired right up.
otherwise, the main grounding at the back of the engine case should be checked. Take it off, clean and sand and reassemble. It is it a great location for unseen corrosion.
this is a long shot, you said that compression is good, for how long? does it hold for a long time? or bleed over a few minutes?
05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter
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