On my bench, I started to template-out my Heads in order to portmatch the FAST intake.... But then I got thinking - shouldn't the portmatching of the intake be done AFTER the heads have been installed onto the engine - in order to properly account for any smaller HG thicknesses, milling, and whatnot?

If you went with a .010" thinner HG, and a .010" mill on your heads, then each intake-port would be "shifted" .020" closer to the block. Thus, the roof and bottom of the heads' cathedral ports would be shifted in relation to the intake manifold's ports - and any mismatch at that time could then be marked and epoxied/dremeled to match.

Is my thinking correct?

 

Yes, check this thread out also.
https://ls1tech.com/forums/generation-iii-internal-engine/463971-port-matching-how-question.html