I can turn this engine over by hand on the stand and there is no contact.
well, no they will not contact on the stand, only when everything is heated up and expanded and moving around.....
interesting problem though, I tend to suspect valve float, or the bad dynamics that Ed stated. Howevery why only 3and 7. Are the spring hights the same as the others, seat pressures.? Is the valve lash on these cylinders changeing ?
Have you tried swapping the heads from side to side to see if the problem follows the head?
Just a few random thoughts here, as I am sure you have checked everything you can think of. I know how you can run around a chase your tail over these types of problems that dont make any sense, But I have usually found there are simple solutions to major problems.
good luck with it