How to clean a classic car engine of rust?

I have 1962 ford falcon with the original straight 6 engine never been rebuilt. So i'm working on it from the top to bottom. First my friend and I drained out the radiator and it was completely gunk and rusty. Its currently off the car and I noticed that rust has gone to my engine. Does any have any recommendations on how I can clean my engine out and how.

If you mean rust in the waterways you flush the engine out with a garden hose until it runs clean. Then you can buy radiator and engine flushing chemical. You run the engine with this stuff in as directed then flush it all out again. A residue of rust in the waterways will have no effect on cooling. If you use 50:50 antifreeze and water on refill no further corrosion will take place.

Engine needs to be torn down and rebuilt. That's the only way to "clean" the engine

Cascade automatic dishwasher soap works good. Put radiator back on. Mix half a box of Cascade in a gallon of water and put in radiator, then fill rest of way with plain water. Turn on heater and bring engine to operating temperature. Drain out, let engine cool, then do over with other half a box of Cascade. Drain out again, let engine cool so you don't crack a head by putting cold water in a hot engine. Fill with plain water and bring to operating temp. Do the fresh water thing three times. Be sure the engine is cool before each time. After engine is fully flushed, you can put anti freeze back in. Since the heater and block are pure water, put full strength anti-freeze in radiator. Should be about the right strength when engine is ran. Be sure to only use Cascade dish soap because it doesn't make suds. Works pretty good. Its what a lot of diesel mechanics due when an oil cooler goes bad and gets engine oil in the radiator.