I can only think of two big things right off the top of my head:
-Listen to the engine idle for the nefarious, sleeve problem. It is evident with a slight knocking noise that is contemporary with the RPM's. This is where the cylinder sleeves have broke loose and begin moving slightly with the pistons. I don't know if there is a particular vintage of DII (mine is an '02 without any trouble; knock on aluminum) that is more problematic than others.
-I have heard wicked stories about the tranny failing. However, I think this is directly related to the way it has been serviced/driven. A quick spin, with the tranny in "Sport" mode (look just south of the shiffter for a button that says "Mode"; push it and the "S" will light up in the dash).
Other than the: Back door handle seizing up about every 4 months, the power seats not working on the passenger side, the clock light bulb burning out in the dash, the jump seats never working properly which has led me to always leave them down, the stupid way that the oil filter was designed around, and the stereotypical leaking of anti-freeze in the passenger seat footwell; it is a great truck!
Hope this helps.
Gary
"I can't believe I'm sitting here, completely surrounded by no beer!" -Onslow