Well, I'm glad to hear my cam wasn't the low hitter

How I would work around the port alignment issue is to just get away from the OE valley pan gasket. Slightly widen the port opening, and raise the roof a little to allow you to tweak the openings on the manifold to match.
It would require disassembly of the heads, but on a race engine that's not really a big deal.

For a typical s/s deal, just bolt them on and don't worry about it.
As is shown, Andy is making 685hp on pump gas with the mismatch in place.