How do I measure cylinder to see how much has been milled off???

That is a great write up and I will be saving it to my favorites on my computer. But cc'ing won't help in my situation. I have aftermarket valves that look nothing like factory. The reason I need to know is my intake manifold is not sealing good and from what I can tell it is not seating far enough down between the heads to get a good seal. I suspect the heades have been milled, which would bring them closer together and not let the intake seat correctly. I have had this engine since 1975 and my dad was the first to go into it and there was no milling done to my knowledge. The stock intake sealed good until it was parked in the early 80's. I had them reworked when I went into the engine. No one at the machine shop I use mentioned doing any serious milling, so I just assumed they just surfaced them.