First off, don't be sorry for the long post. It's better for us to get the most detailed idea of what is going on and for you to get your point across as specific as possible.
I'd suggest not doing an engine flush as they can cause more harm than good most of the time. Especially with 89,000 miles on it, I wouldn't do an engine flush. However there's a product out there called SeaFoam, works wonders. I'm not sure if you're familiar with it but it's a safe alternative to an engine flush and, for the way I use it, only goes into a vacuum line and the gas tank. I am scared to put anything other than oil in my crankcase just because I'm not sure what exactly it's doing in there.
If you want some more information on SeaFoam, check out their website, http://www.seafoamsales.com/motor-treatment.html
I would run that thru the system and if you haven't used it before, I'm warning you that it requires to be in an open area preferably at night. I am inclined to believe the water on your filler cap is perfectly normal. I have heard of it happening before and only in the winter months.
I once had a customer come in one time with the same problem and we ended up calling up the dealership locally and the tech on site told us it was normal. I would do the SeaFoam thru the engine to be on the safe side however.
If it was more of a milky foam however, there is a TSB for that. It is 09-01-00 Rev. A. The Title is : "Foamy Oil Emulsion Accumulation Inside The 4.7L Engine Oil Fill Housing". It is dated Sept. 11, 2000.
It says to replace the oil filler cap with the two following parts:
53032389AC - Baffle - Oil Fill Housing
53032126AA - Cap - Oil Fill Housing
To make sure it's not a blown head gasket (I wouldn't trust anyone at Jiffy Lube but that's just me) keep an eye on the coolant level and make sure it's not dropping. Also check periodically under your vehicle after you leave it siting for a while and make sure there's no coolant on the ground.