Hughes rocker arm pedestal shims

Shadow said

I've actually also wondered if the machine shop knew they were going to mill the heads if they should have accounted for the difference with the installed height of the valve stems themselves. If they were to be surfaced a bit too it seems like things would be way more in line but to mill the heads but leave the valves at stock length already throws things off right from the start.

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Milling the gasket surface has nothing to do with the stem length or valve job.
These are what can affect geometry on a Mopar shaft system:
-The stem heights are a result of the valve job: the seat depth, the seat cut on the valve, and the stem cut of the valve. Those are all set during the valve job.
-The rocker shaft centerline position is set by the factory and unless you replace the stands with support blocks, it never changes.
-The rocker's tip position may vary depending on the rocker manufacturer.

What I would suggest is you get a pushrod checker. Thread the adjuster down so there's 1/2 a thread showing and then use the checker to determine the length you need (and don't forget the proper lifter preload if it's a hydraulic tappet). Then call Manton or Smith Bros. and have a set made and delivered to you.
Pushrod length is one of the innocent bystanders of head milling to gain compression. If you go too far (and again - that's from the factory original surface... not the surface you may have on your heads if they were cut once eons ago) then you have to start buying parts to get things to work right.