New EQ Head port misalignment?

PRH said

I thought you measured the port locations and saw the bottom of the EQ port was like .200” higher than the stock head(.675” vs .450”).

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Correct. This was measured from the deck surface. Measuring the deck to the bolt holes, it seems to be in about the right spot.

Just because the ports are off doesn't mean the bolt holes are. I am betting the bolt holes are referenced off the deck, not the ports.