How do I get rust out of my fuel system for a Ford 1996 F-350 diesel?

The best way is to remove your tank and get it chemically dipped at a specialty shop.

agree with #1 as thats the only way to get all the debri

Chck price on aftermarket replacment tank. Do you have your own (private) fuel supply? Or does it sit around with say 1/2 tank, or less, of fuel. Unusual problem on a Diesel, at least at at my shop.