sorry to hear about your wasted 502. By the sound of things it almost sounds like a hydroloc situation. If you pull a bit of water into a hot cylinder it can expand pretty damn fast, especially with the added compression of the motor. I have heard of valves getting pushed up into the head from the pressure and typically something lets go to relieve the pressure. Perhaps in this case the piston deformed under the stress as well as the valves. That would explain your scored cylinders, mushroomed valves, and deformed pistons. What it doesn't explain is the head gasket. If the gasket was bad it could be the cause of the condition, but that still wouldn't explain the evidence of excessive heat on the gasket.
The other possibility is that it was indeed excessive heat in the #3 and #5 cylinders. Since I believe these are siamesed in the 502 it does make sense that if a water passage was blocked or filled with sand around one, the other might suffer through conduction of heat by the block. While you might see a stout 502 with jetting richer than 86s in the rear, I don't think its lean to the point of being your culprit. When your machinist goes through your block, see how much sand comes out when they flush it. Hopefully that is your answer.
Good luck and keep us posted,
Chris