I'm just getting into this one... so I'm sorry if I recommend things that have already been tried.
Much if what you've done troubleshooting is sound, though some of the replacements add a few variables. I'd go back to the original CDI and reattempt, if you haven't already. You located a ground through damaged insulation in working in the frame. I assume the stator windings have a varnish on them of sorts that provides insulation to the windings. I would thoroughly inspect it and do a ground check to ensure it is not a path to ground. If there's a way to check continuity, it'd also make sure the winding isn't open. It's hard to see an open on a set of winding. When I've seen them, it's been in generators that are reverse powered, and then... if you can see the defect, it's on the first turn of the winding. If there's a thicker portion of the stator that is essentially an output terminal, it'll usually thin out where the winding starts, and that's where you get it.
You've replaced a great deal. W/just a multimeter and not a megger, it might still have a ground issue depending if the voltage that is going to the plug are sufficient to punch through a spot in the insulation. I'd look at the plug wires as well (I'm sure you've done this) and not all plugs are the same... Ive seen some of the plugs touted to be gy6 plugs have too small of a terminal causing the plug to have no spark. If you're getting the starter to turn it over and power to the accessories, there oughta not be much left. I'm a navy electrician by trade... while I've not had to troubleshoot a gy6, there's not a lot to them. I think you're close and solved the big issue of bad wiring grounding to the frame. If you can disconnect each component and do component level troubleshooting, you can rule out ever individual component. Again, you getting new parts are all variables (though I'd of done the same). I'd check each component.
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