intake/exhaust mounting, what am I missing?

For sure you are missing three standard nuts (top row), and one each of the cone washer and goofy tapered castle-nut looking nut (middle row, right side). IIRC working on my feeble memory only, there is a somewhat oversize brass washer that goes on the top middle stud, you are missing that too.

I can't get outside to refer to my books so I'll let someone else weigh in on the studs and where they go. You are showing 14 studs but you only need 13 total. Be aware a couple of these go into the water jacket so the studs need to get sealant on them before installation.