intake/exhaust mounting, what am I missing?

Dne007 said
Yes, Zach and I had a discussion about it. That bolt does not go through the exhaust manifold, like it's made that way. I'm no way an authority on this;)

Here you go. Here's a nice article showing you exactly where and how the hardware installs.
https://www.slantsix.org/articles/manifold-install/types-mounting.htm