I asked about rust when I took the block in to get it cleaned and the shop said their hot tank did not clean rust. What to do?? If you have the engine out opening the core plugs and mechanically scraping and blasting will get a lot of it. The mutatic acid might get some more. What's left you could neutralize with the kind of expensive but good "Rust Cure."
However, after all this one day I drained the water from the radiator and it ran red like Custer's last stand. So my final recommendation after all the cleaning is to immediately put some kind of rust preventer in there or it will happen all over again.