You may have better luck asking the 5.0 forum instead of the 4.6 forum.
But that's the kind of job that you could have quotes an order of magnitude different. Some shops may not even touch it because they wouldn't warranty rust repair, while another guy may give you a very cheap price just to weld a piece of sheetmetal on.
Either way, not much use asking here. If you want a quote for work, you'll have to start getting quotes from local shops.
So is there actual holes or is it surface rust? If the metal is solid grind off the rust and paint it with POR-15 or something similar. Do not worry about making it shiny knock off the surface rust POR-15 adheres great to rust.