Intake leaking, heads milled?

You shouldn't have to pry on the manifold at all to get it to line up.

Ask the machine shop what their "resurface" means.

On a big block Chrysler .0123" should be removed from the intake side of the head for every .010" from the combustion chamber side. Stock, the head should be about 1.000" thick where the short head bolts go through the head on the exhaust side.

I would lay the intake on the engine with no gaskets in place and check bolt hole alignment. Using feeler gauges, see what clearance you have on all four corners, top and bottom of the intake. If the intake manifold bolt holes are high, the head intake side or the intake manifold must be milled. We sometimes have to do some angle milling of the intake to get it to line up parallel with the heads.