I bought a 440 crate engine and have had cooling issues since installed, went everything that we could come up to fix but no luck. Tore the engine down and found that the head gaskets did not have holes in them between the cylinders on the lower side of the block. One guy didn't think it was necessary to have the holes and the only gaskets that I can find that have the holes are copper, what's the general opinion?

 

Put up a picture of the holes your talking about.
in the seventies mopar added holes in the rv heads then in all BB heads but not having the holes in the gaskets usually isn't a problem.
The overheating problem could be from late timing, I find 440s like timing, it's not uncommon for the bbm to want 20 degrees advanced initial with it 40 degrees all in by 2500 rpm.. Aluminum heads will need less total timing 33 to 36 total.
what are you using for a water pump?