Ford doesn't recomend Bio-Diesel to protect themselves from the unregulated "Home Brew" fuels. Ford also doesn't build the diesel engines they use either.

The Soy Diesel you buy at the pump is safe to use in your diesel. It has to meet the same minimum standard as any other fuel being sold. Soy-Diesel is better for the environment because it uses the Soybean oil to replace the sulfer as a lubricant. Soy-Diesel will also help clean any your tank (this is what can plug your filter the first time you use it. Not the Fuel, but the dirt that was in your tank already.) Our FS runs there fuel tanker on 100% Soy Diesel with no problems.