intake alignment?

I have a weind stealth intake that cam off a motor that had been squared and decked,pistons came out of holes .020 and the heads had been worked,ported, polished,and milled(not sure how much)I,m trying to figure out if maybe they cut the intake down to match that work.when I put it on my engine it seems to narrow.the gasket seal line on the intake gasket sets high enough on the head that it shows above the intake.any ideas of how to check this? Thanks for help.