Thanks for asking all!
Been driving it on the stock tune this week to see if I can figure out what's going on with it. I'm thinking about paying the dealership to do a compression test with the idea that, if it shows a problem, they can bury the paperwork. If it come out fine, then I will have peace of mind and pay for the test. I could do the test myself, but I need them to have the results as well.
Here's where it stands...
- CAC cleaned about 3,000 miles ago and showing clean still
- cleaned the IAT and MAP sensors
- new Motorcraft plugs installed, gapped at .030
- stutter is predominantly when in 6th gear at 1400-1500 rpm, but it does do it randomly in other gears
- it also sometimes hiccups/stutters at low speeds on deceleration (this one makes me think PTU)
- idle quality is poor. I don't have a point of reference from other 3.5EB's, but my idle quality is better than performance cars I've owned, but no where near that of a factory Honda, Toyota, etc. This is, however, also the only car I've ever owned with a 600 rpm set idle. Didn't even know a car could idle this low. LOL
- car doesn't pull any codes, but I saw this on the engineering screen...

Do your cars idle like silk at 600 rpm? Mine bounces between 600-650 like it's not happy idling that low.