Full Disclosure: I broke the "1 mod at a time" rule and put in a lowered seat frame and R6 rear light at the same time, both of those work perfectly so I can't imagine they're related
the one mod at a time thing is for performance mods, cosmetic mods don't apply.
I was being a smartass, I know it shouldn't matter. I went in today to finish grinding off the rear tail light assembly, while there I opened up the bbox and re-wired all the connections to the CDI. Re-wired as in soldered every connection and used new 16 gauge wire for each to bridge between the CDI and the Relay (so that there was some slack in the lines to remove that as a problem). Just ran to get some gas and it ran just as shitty as before.
On the plus side I know I didn't fuck up any of the wiring I was worried about fucking up (not wanting to lose my electric start meant I had the fear of god in me hooking that thing up). Bad news is it still runs like piss, which means it's got to be the coil hookup causing problems. I'm pretty sure I wired it up correctly (and got the connections in as far as they could) though.
Unplug Coil wire->Connect CDI->Plug Coil wire into CDI. I made damned sure it was the right one i disconnected (though if I got the wrong one I'm pretty sure I wouldn't be starting at all), so I'm not sure what's going on. I'm going to open her up again tomorrow when I can see again and redo the coil wiring, hopefully that solves the problem...