The larger head will make a slight difference but I don't think it will solve the problem, if you still have the engine in pieces, check the cylinder ports, I once had an F200 that kept overheating, I took it to a specialist 2 Stroke engine re-builder, he told me the ports were not rounded off, and were catching the piston rings, he suggested I smooth them off with emery paper, I tried to do this but the Nikasol coating was too hard, so I told Patricie at Walkerjet and they sent me a new cylinder, the problem was solved.
A few years ago there was a problem when they first changed to digital ignition, the ignition advanced too much when on full revs this caused the engine to get too hot. A few of these were sold, when Walkerjet discovered the problem they offered too replace with the standard ignition, until they solved the problem, it is possible that you have one of these with the problem ignition system, how old is the motor?
I think you should send all information to Patricie at Walkerjet, and ask for their advice and help, they will know about all these problems, they are very helpful, but take a very long time to respond, it may take months to get the problem sorted, so if you can afford it buy another engine.
Paul D