What a frustration that carb is!
I can't believe that they took the time to shave the fasteners. You're gonna love the Mikuni.
Your bike is the most advanced that I've seen so far; I've never seen a removable subframe before your video.
You can use the existing airbox and filter cage with bulk Uni filter. it's good stuff, and you can usually find it at the local bike shop. I use Maxima Fab1 spray oil on my filters. It goes on blue and sticks like cobwebs.
Instead of buying a bolt kit, I bought assorted stainless socket head cap screws from a local fastener supplier. My thinking is that I can carry an allen wrench, rather than sockets or combination wrenches. Plus, I'd rather have stainless.
Is that a stainless header?
Have you set the valves yet?