Mini update (sorry no pics):
Got my brake pedal installed. Gently sanded off some of the powder coat, got a snug fit, then applied some moly grease to the pivot. No wobble - all set.
On the engine side of things I have both crank bearings installed in the cases, and am holding off on a couple smaller bearings from Kaw before I assemble. Hope motojason will follow up to my question above. Or I'll figure it out.
Debating whether to get a new airbox and boot.. what I have isn't perfect, but that's another $160 in parts that I probably won't recoup.