Intake manifold won't seal - How do I check it ?

How much are your heads milled?
For every .010 off the head you have to take about .012 off the intake to get it to align properly.
How do the bolt holes align?
How is the alignment with no gaskets in place?

To my knowledge these heads have never been milled. They have been in the family since 1975 and retired in 1980 until recently when I took them to be reworked. Bolts holes alignment is good. I am going to check the intake on the engine again this evening to see if I can see any alignment issue at the bottom.