make sure you can run the bolts down in the holes without an intake on it of course you just took them out so that shouldnt be the problem. you say you tried it with no gaskets?
haven't tried bolting the intake down without the gaskets (I probably should have LOL). If I remove the intake can I re-use the gaskets? It has a little bit of RTV around the water ports and it has the gasgacinch (or Canadian equivalent) on the head flange and the head side of the intake gasket.