My oil burning pig. Pics too!

nm9s - what you're seeing as off angle I'm seeing as the intake is too fat for the valley. Make it thinner and there will be crush on the bottom of the gasket. That's assuming all the ports have that same issue. If the issue is apprent only two ports of four on one side, or only all four on one side but the other's fine, the I'd agree it's an angle issue too.
If the head and intake angles are mismatched all across one side or the other, then just shaving the manifold at the existing surface angle won't close that resulting gap at all. The plane of the intake and head surfaces should theoretically be an exact 45.0 degrees from a vertical plane through the engine; if not, they should be matched to at most 0.1 degree tolerance, probably less; every 0.1 degree off of a perfect angle match results in about a .0035" gap opening at top or bottom.

OP, hope you have the solved! What a saga.....sounds like you should do the standard checks of the intake manifold fit with feeler gauges and clay. Seems like we could all use the equivalent of Platigage for manifold fit checking to check gaps all around.