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Here's what I do.
If the cooling system has had a soluble oil in it at any stage, it will first be necessary to remove the oily film it will have left so that the vinegar can do its work.
I use a tablet from the dishwasher for that. It cleans well and doesn't foam up like most other detergents.
Then, I use 4 litres (about a US gallon) of vinegar topped up with water and run the engine till warm to get an even distribution of vinegar and water throughout the system. Neat vinagar won't do any harm. You may use the car as normal while the vinegars is in there, in fact, I believe it is good to do so. I leave it in for about a month, depending on how bad the rust is. When draining the fesulting soup, be careful - it will stain anything. Drain, flush a couple of times and refilll with your usual coolant and you're done.
If the car runs at what you think is too hot, back flush the radiator. It may have some rubbish in it from the process.
You'll be amazed at what comes out.