Valley Baffle Clearance

I just purchased a Milodon lifter valley baffle and I'm having some contact issues with the bolts that they sent to secure the hold downs to the valley baffle. They sent hex head serrated machine bolts and the tops of the bolts contact the bottom of my intake manifold. I switched to some serrated machine bolts with straight blade screw driver heads and ground a little off of the top. I dry fit the heads and intake and it seems to clear, but I want to be sure. Any ideas on how to measure the clearance?

If I get a chance I'll post some pics to illustrate.