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 cocked 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 ?

Mine's pretty rusty in the coolant passages.  But it has never been a problem.   If it looks like chunks are going to break off and be floating around, then clean it out like carlsjeep said.   When I was rebuilding my engine, I found a length of wire coathanger inside my block.  I think the previous owner was trying to use it to scrape off crud in the passageways and dropped it and just left it.  I pulled it out during my rebuild when I saw it through one of the exhaust stud threaded holes.

Evapo-Rust does work but you have to get all the loose rust off before it can do it's job.

Bob, now that is something I would have never guessed or thought about.    Now that you mention it, I am betting that was the source.    I wonder if I should put it back in my block for authenticity?