Originally Posted by techinspector1
Don't worry about it until you install the motor in a vehicle and have it running. Then, use a commercially-available cooling system cleaner such as this one to remove the rust.
Cooling System Flush
Should work good.
You could just flush it with regular water after the engine break in first oil change and again after a few more. Flush would probably be better but i have alway just used water. If its really bad i take out the thermostat and stick the garden hose in the hole and let the water run with the lower hose taken off. Thats how i have done it every years when there is no antifreeze and tons of rusty water come out every time. Same for the radiator. You may want to use some shop air and blow it out before install. Or even run some water through it on the stand if it was put up wet and has seen some moisture without covers. Also check to make sure bores are clean. Little oil goes a long way.
You can also open all the water passages and freeze plugs and clean out any way you can if its really bad.