New intake sitting too low, exposing the exhaust port!

[Severisth]

Just bolted up a ported stock intake, and it is exposing the EGR port on the stock heads, which makes me think it is sitting too low. What could be causing this?

So far, I have ruled out the following:
1. Intake milled. The gentleman I bought it from guarantees it hasn't been milled.
2. Gaskets wrong. He used it with 1250 Fel-pros, which are stock thickness. I put some 351 gaskets on it, which should be the same thickness.
3. Gakets slipped. When I installed the lower, I threaded in some studs on all four corners and set the gaskets down on the studs, then the intake. This should rule out movement of the gasket.

Any other ideas?

[Shaggy]

The only time I have ran into that is on some aftermartket intakes (IE: sheet metal) Or the intake milled to match milled head/block. Other than that I don't what to say...unless the 86 lower is slightly different in that area as well as the runners being different.

[Severisth]

Turns out it was just an empty casting boss. The car just needed the MAP vacuum connected and the computer reset. :D