There is some more information that is needed. Are you running steel rods or aluminum? Timing chain or timing belt? Are the piston valve reliefs at the same angle as valve angle? How many RPM's are you turning?
When you are checking the piston to valve clearance are you checking on #1 only or on all cylinders and what value are you coming up with? I try to have .100" for the exhaust valve as a minimum. 10 degrees BTDC of the cylinder checking is the critical timing for the exhaust valve because the piston is "chasing" the exhaust valve closing. It is 10 degrees ATDC for the intake valve. I usually like to advance and retard the camshaft 8-10 degrees (timing belt makes this easy) to check this clearance, also. That way if I want to advance the cam 4 degrees, I already know that there won't be interference problems.
The margins on the exhaust valves for #3 and #7 could be thicker which could put those valves closer to the pistons to begin with. When you had the heads shaved you would actually make the problem worse, because the valves are getting closer to the piston by the amount you have the heads resurfaced. The timing chain could be stretching some or the camshaft timing could be off some on those cylinders or it could be twisting some. The deck height is stated as .005", has that been verified on every cylinder, because they can sometimes vary a few thousands from cylinder to cylinder.
Since you are having recurring problems, I would check the piston to valve clearance with the rocker shaft numbered for each cylinder head and verify the rocker ratio for each. If all of the numbers still measure up, then I would flycut the pistons and increase the piston to valve clearance by .040"-.050" as long as the piston decks could handle it.
This is just some things that I would check and I am sure that there will be some other good inputs on this, but we will need to know what is the exact value that you are coming up with for the clearance.
Bill M