Try these chemical rust removers
I am trying to save a 289 cid Ford engine in a 1966 Mustang. The engine was rebuilt and then stored for 19 years with a dry cooling system. Now major rust is in the water jacket that scales off at operating temperatures. I have tried three different chemical flushes, and ran the engine with a garden hose filling the radiator, and top hose disconnected at the radiator. The engine did not have a thermostat in at the time either. After doing that I still get pieces of rusty scale large enough to plug the radiator. Do you have any suggestions other than pulling the engine and having the block boiled? The engine is rebuilt and has an aluminum intake manifold.
If you ran enough water (preferably hot water) through the engine, all or nearly all of the loose scale would eventually get washed out. I have never done this so I can’t say that it does or doesn’t work from my own experience, but something else to consider is the application of a chemical rust remover.
After draining the entire cooling system, you can disconnect the radiator and heater core and plug the relevant ports to isolate the engine. Then, pour a chemical rust remover, such as EVAPO-RUST (evaporust.com) or Inter-chem Rust Remover (interchemfirst. com; 800238-6531) into the engine and let it soak for as long as the manufacturer recommends. Drain the rust dissolver out, flush the system with lots and lots of water, reconnect the hoses, and fill the system with a 50/50 mix of distilled water and antifreeze.