Going 05 or later is a good idea. They revised the front suspension in 05. Added coil springs, rides a lot nicer. Also tightened the turning circle. The issues were with the 03 and 04, and these were shop and parts issues, not a design flaw in the engine.
Don't know if there's a specific way to find out if the engine has had a tuner, I'm sure Ford would like to know that, as well. If the truck has other mods: larger exhaust, extra gauges, cat bypass, larger wheels, etc... then it probably had a tuner.
You don't tend to see duallies modified much. Mine came from a farmer who was pulling a gooseneck livestock trailer with it. Been very reliable. Blew a HPOP seal about a month ago, that's the first trouble I've had in two years. Fixed under warranty, they paid the tow bill and even changed the oil while it was in the shop.
I've left mine stock, got plenty of power for what I do. Modded the sound system, instead. Pioneer nav unit, JL Stealthbox in the center console. Goes 0-120db in no time at all. The new Tom Petty album sounds great on it.