Pilot light on a Pentair Pool Heater won't stay lit?

Sounds like you have dirt in the supply line/valve. You didn't mention if the pilot goes out suddenly or slowly fades. This might give you a clue to the source of the problem You have been thorough with your trouble shooting procedure. I would try removing the gas valve assembly and thoroughly inspect the connections for dirt and corrosion. Try blowing compressed air in the opposite direction to normal flow. If there is an adjustment to the pilot light height, your problem could be in that circuit.