It seems strange only 3 and 7 touch.
one of the deals may be, the head guy resessed some of the valves up into the head and not others. did you cc the heads ?
the only other explanation would be the camshaft is ground wrong, have you used a dial indicator to see how much of a lift at full open you get?
hmmmm
another thing, what crank is in it? Could crankshaft deflection be an issue?
maybe crank is slighly twisted.
Al