If you have a wire wheel on a bench grinder, you can probably get most of the rust off. Careful with the gas though.
I would try to vacuum most of the rust off the head first. Again, careful with gas vapors and a vacuum. Then you pour kerosene or another cleaning product down the oil galleries in the head. There are a multitude of cleaners at Ghettozone, but most are designed for use with the engine running. For flush, I would just use kerosene. The kerosene will end up in the oil pan with all the other particles, so you should drain then pull the pan and clean it before use.
Once you get the engine installed, put a couple of quarts of fresh oil in the motor. Crank the engine over with the coil wire removed so it doesn't try to fire. This will get the kerosene out of the cylinders. Drain the now contaminated oil and put on a new filter and new oil in.
Once you get the engine running, tuned and driven for a little while, you should check the oil again. If the dipstick smells like kerosene, then you need to drain the oil again.
This process will work, but takes some time. I did this on a 4 wheeler engine that was full of sand from drowing in a creek. That was 5 years ago and the engine still runs and doesn't smoke.