Are you sure your block was never decked and your heads haven't been milled? With a new intake it would be frustrating to have to modify. But if things aren't coming together properly in your mockup install you have to do something. You may consider using the extra thick intake gaskets. Mock it up, if you're not having success then either send it back (if they take it) or drill out the holes. Can you get a mag light and look down in there to figure out what the obstruction is? Is the bolt getting hung up on the intake gasket or is the hole too far off center of the threads?