Buy one of those $9 IR thermometers, run the engine as hot as you possibly can (but that you could do only on a hot day in the middle of the riding season) and take the temperature. Then research what prep and paint options you have available for such temperatures. At best you will find a product, at worst this would need powder coating or something that you cannot do yourself or cannot do without disassembling the engine. I mean, to do it properly. You can always hide it temporarily so that it will flake again soon.