gt-40 heads and track heat intake, why wont it fit?

Went to put my intake on this weekend and the lower intake is hitting the edges of the heads so it wont sit flush. does anyone else have this setup. Im wondering if the machine shop took to much off my heads and block. This is really gay. try to get pics up later.
 
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You can have the intake milled to match - Find out how much was taken off the heads or if the block was decked a significant amount...

There is going to be a little gap, from the intake swaps I have seen...

The end gaskets/RTV or RTV should fill the gap fine...
 
yeah both the heads and block were machined. something is definatly not right, like I said ill try too get some pics up by this weekend so you can better see what I mean. its not that the intake isnt coming down flush with the valley, the out side of the intake where the ports are are hitting the heads not letting the intake come down flush. are the heads suposed to overlap the block a little on the intake side.
 
is this with or without the gaskets inplace? the gaskets should compress a little depending on what kind they are. try and see how far down it goes with no gaskets