Well, I'm on broke-mode, so I went to harbor freight, bought a timing light and got to work. And man did I learn a lot today playing with that light!
I spun the timing plate counter clockwise a little bit to get the F mark to line up with the casing mark and went to work. After rechecking the gap I screwed everything down and back together went on a test run and not only did it run better, my tach actually swept past 4K for some reason. The bike still seems to stutter at 3/4 to WOT though, which it DIDN'T do last week, and the sound from the intakes sounds like it's drowning or something. The bike will pull (eventually) past 80 which is as brave as I'm to take it.
So, power is back, but something is still up...