Thanks Guys,
A most interesting thread - before posting the question I simply assumed all engine bays had the holes. Possibly because I am mostly looking at photos '69, '70 & '71 engine bays. Just getting back to my original questions - I am thinking :
1) I might get the engine bay sprayed without the rubber with the plugs so as to cover all metal (even though it wasn't done that way originally). IE: Try painting the rubber plugs - if it looks OK, I can leave them painted - if not, it should not be difficult to remove the paint from them (or simply buy more plugs). I would say nearly 100% of the restored engine bays I have seen have the rubber plugs unpainted. As much as I like to have it original looking - I'm not into recreating shoddy work.
2) Still don't know the original finish on the engine block blanking plates and don't really care anymore. I cant imagine I will remove them so I might give them a spray with HT Silver paint in place. Defy anyone to see more tan a glimpse once the engine bay is complete.
3) Will go with natural finish (Clear Cad) on the vacuum brake lines.
4) Ditto on the ignition coil bracket and filter hose clamps
Cheers.