99 4.0 - running rough - shales at idle and highway

[99_4x4_Offroad]

I am the original owner of a 99 4.0 XLT w/ 68,000 miles. Being in the military I'm never around. When away I have someone drive it about once a week. 18 months ago I was toid it was running rough and had it taken to the local dealership. They stated the headers may be cracked (no further infromation). I told them not to worry about it and I'd take care of it when I returned next year because the truck was not being driven. I returned and have been driving the truck with no problems for about two months. I chalked the problems up to moisture buildup in the gas tank. I recenlty left again for a month. This time my ranger was not started for the entire month. When I started it, it began running very rough, lots of engine shaking on the highway. The check engine light came on at this point. I drove it straight to my dealership. They called this morning stating the diagnostics indicate possible cracked headers and it would cost $750.00 just to pull and inspect them. Is it possible I have water condensation in the fuel tank due to length of inactivity?
I would love to hear some reccomendations or advice prior to speaking w/ Ford when I pick up my truck. I will post additional information after speaking with Ford techs.

 

[CaptainStomp]

My 94 4.0 liter/v6 ranger xlt does pretty much what you mentioned, but only after driving for about an hour, and seems to run fine after I let it cool down. I've never been told it may be cracked headers though. The problem I have was more severe and would even stall while I was waiting at a stop light, but was reduced to pretty much what you explained after my cat, o2 sensors and a heat sensor where replaced. 4-5 years ago I remember my truck was having some really rough starts, and somes wouldn't crank over at all, but seemed to fix itself. I've always wondered if the problem I have now is somehow related to that old problem. Oh yeah those are some nice boobs in the picture by the way, whether it's you, your girlfriend or someone completly unknown.