Vacuum on 1968 GTS 340 4 spd.

I would also try checking the lifter preload, not much else at this point. I can pretty much guarantee with your Eddy heads and new head gaskets the pushrods need to be a different length, most likely shorter. Were the heads milled at all? I kind of hope so TBH, I have a pair of Edelbrocks that just got done and my machinist said the decks were super crooked, had to take off .008" to make them flat.

If the pushrods are long enough it could be causing some of the valves to hang open just slightly which would make sense with the low vacuum and weird running issues.

OH yeah and once this is figured out get a new harmonic damper on there pronto, from here on out the outer ring will just keep slipping which is no bueno. You'll keep chasing timing marks that move and the crankshaft might eventually get damaged.