Hopefully this is just an easy thing I'm overlooking.

On my Eddy Air-Gap intake, there are two bolts that don't want to fit. They are the two middle ones on the passenger side. Should I be using studs there? Or special fasteners? Maybe it's something obvious I'm missing.

You might need to elongate the manifold holes slightly but first I'd check the bolt hole/manifold alignment on all holes as they might be borderline & either need a thicker or thinner gasket or manifold milling depending on if the manifold sits too high or too low. Good visual & go from there. & Ideally it's the port alignment that you want dead on rather than the bolt holes as you have a slight leeway on the bolt holes.

LA or Mag

The two center bolts [ LA Air Gap ] can be difficult to start due to the way the ports are shaped. If all of the other bolts go in without much problem it will help if you grind some clearance notches on the outsides of the # 4 & 6 ports so that the bolt heads will go in straighter. Like Robert said, make sure the manifold actually fits first. Often times if the block has been decked and the heads milled the manifold will be too tight a fit unless the intake side of the heads was also cut.

LA Air Gap, yes the bolts adjacent to the 4 and 6 intake runners.

Ugh, I hate grinding on brand new parts. You would think that they would've seen this issue in product development. The intake does match the block and heads just fine.

So I guess I will start with ovaling the bolt holes and see how far that gets me before notching the runners.

Glad to see I didn't buy a defective part. Just a known issue.

I don't like having to "make" parts fit either, but you may as well get used to it. Just part or the "joy of hot rodding". It only gets worse the more exotic and expensive the parts are.

There are other intakes that have same issue for what it's worth. I usually buy new intake bolts that have smaller bolt heads similar to a header bolt. It makes things a little easier
Keith