John Deere B cooling system rust

I am restoring a 1947 John Deere styled B. I decided to remove the exhaust manifold to clean and paint. I had to remove the upper water pipe to get the manifold off. Of course being 67 years old, I twisted off several bolts and studs which needed drilled out. While drilling I used magnets to keep the drilled shavings out of the cooling and exhaust ports. A few shavings fell in anyway but I used the magnet to retrieve them. When I put the magnet in the cooling ports, I was getting big chunks of rust on it. I have installed a new radiator on this tractor and am concerned all the loose rust in the system will plug the new radiator.
Is there a way to flush the rust and dirt out of the cooling system before I connect the water pipes to the radiator?
Thanks,
Bob
 
Phosphoric acid and a tank to put it in will clean those parts out. You can get it at Lowes/Home depot.
 

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