Great reviews. Glad you're loving the bike.
I ran Moose Racing footpegs on my XC last year without even riding teh stockers, but I never had an issue with the kick lever. Nevertheless, care to share the Yamaha part number for the kickstart?
The filter setup is a little odd (too close to the subframe at the top in my opinion), but after a few changes the foam takes a set and you're in. Just remember that the "up arrow" actually points closer to 1 o'clock than noon
It doesn't hurt to run a PC Racing neoprene ring in the box either - seems to help alignment and sealing.