New EQ Head port misalignment?

At one time I was going to try and make drilling jigs. Just what WOULD BE a "zero" reference point for everything else? I mean, the deck surface can change, so would you start with the valve spring seats? The rocker cover surface is a casting so that is not exactly a precision starting point.
Deck surface would be my datum IMO. sure it may change a few thousandths if machined but gaskets have tolerances that a .010 skim can soak up.

And looking at the intake gaskets, they have tabs that align them up and down from the deck surface and left and right based on the headgasket. And the headgasket is doweled to the block/heads