UPDATE2: They determined the dirt and spots can't be cleaned and I will be getting a whole new headliner!!
On a side note, after a tire rotation and alignment, I have noticed resistance when driving. Service center thinks it's the brake caliper pins. They are replacing those as well next week when parts arrive. Downside, they messed up, upside, they are fixing their mistakes!
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Glad they are taking care of it, seems like you have a fairly good service center. The nearest Dealer to me is a "mega" dealer which has its perks but the Service advisors and managers are just in a rush to get people in and out and there are receptionists in the service center that actually do the typing so you end up with 3 people (not including the tech) you have to explain things to and so much gets lost in translation is ridiculous. I avoid if at all possible, although if you want an ego boost every time you head to the dealership someone comments on the truck.