The holes in the timing cover are "leftovers" from days past. The early V8 cars ('55-'59, anyway, maybe a bit later) use a "front mount" where the timing cover was used to support the front engine mount. I have a '57 347 here from a Starchief with the mount still attached. All the early stuff had a cast iron cover. They MAY have used the aluminum version in the '62-'66 GMCs, can't say for sure.
Which holes in the heads? You mean the 1 3/8" diameter? They're for expansion plugs, and the only "non-threaded" holes in any of the cores here now. If not, what casting number, and a more precise location on those holes?