I with you on that one, I would replace the pistons either. For that matter if I was spending $3000, I'd go a little more and get a remanufactured motor.
Have a shop pull the head and send it out for evaluation and maching it flat. There is a chemical test that can be done to check for a headgasket problem. The chemical is added to the cooling system and changes color if the chemical detects exhaust gaskets.