check your gaskets to be sure they're on correctly.

i know that sounds stupid, but if the 2 inner bolts will not go in, but the other 4 will, most likely you have the gasket on the wrong way, the outer 4 are in-line, and the inner 2 are staggered. most likely why the outer 4 will bolt up, and not the inner 2.

just my .02 on a potentially easy fix.