I dunno, is that a lot of meat taken off of it?
Sorry, I've been out the door for awhile. Meat taken off the heads? Was anything said on the heads, when you bought them, as far as that? You've gotta understand something...motors is a numbers game...measurements! And, what you do with them.
To the tappet stuff (yeah, I'm playing my naming game, again)...meat off the heads, or deck surface are a big effect on the valve train. Period. You take that for what it's worth. The numbers involved are a must know deal!
Okay...metallic noises...something banging together...
Tappets bottoming (via too much pre-load, via too long push rods), valve spring coils getting together, valves hitting pistons...on and on...
Problem is, everything needs to be checked. There's a problem somewhere, and it needs to be found. Yeah, I know. I've been there...
Just to toss a wrench into the works...on the ill fitting intake manifold...sounds like the wrong thickness head gasket (that would put those holes back in line). YES, other things need to be considered, compression ratio, and such. Ya get what ya get.