The bolts do sit very high in the bolt holes. I noticed that the bolts at the rear of the intake actually rub the top of the hole and are difficult to start.
It's a good possibility thicker gaskets will help with alignment also. What I'd do is get 4 feeler gauges and starting with .060" (the thickness of the gaskets you've been using) insert one at each corner between the head and intake working your way up to how thick it takes to center the bolts in the holes. That'll tell you how thick the gaskets need to be. In the case of mine it took .090" to center the bolts. Cometic had some .094" thick so they were close enough to work fine.
Yeah that's them. I used the Aramid fiber gaskets for the intake. There's only one drawback with them, you have to use sealer around all ports so if you ever take it back apart it's more clean up work. Other than that they work great.