I had a 02 F350 that I ordered with a 6 speed manual and all the heavy duty stuff. I couldn't find a dealer that had one. They all buy the same "vanilla" spec truck because they get a discount from the factory for sticking with a common bill of materials. When I sold the truck I found that it was worth it's weight in gold because Ford was having so many tranny failures with the E40D and 4R100. If you can find a 6 speed manual buy it. Or if nothing else keep $4000 in the bank for when the auto bonks out and you have to replace it.
On a newer truck (2008+) I personally wouldn't be afraid of an auto trans. I believe they are FINALLY starting to figure out how to make them hold up
