My father, way back when, put a new thermostat in. Unfortunately, he
didn't put it above the retainer...

So, during my project of getting the Willys running after all those years in the garage, when I pulled the elbow off the engine, I saw the thermostat * sideways in the head. Thanks, Dad, rest in piece, still love ya. When I peered into the head, I saw, what appears to me, to be a lot of rust.
Since I just got my radiator back from being re-cored, I'm not wanting to plug it up. Is it normal to have rust in the head and I'm creating "rot-rohs" that don't exist ? Should I pull the head and have it flushed ? If yes, is this something I can do myself, or is it time for a pro ?
Or just run it (whenever THAT will be..) and keep flushing the cooling system ?