Maintenance is maintenance. All you have to do is get the maintenance done in a timely manner and be able to prove it was done if you have a warranty issue. Keep your receipts and be sure that your mileage is noted on them. If you do your own maintenance, get a log book and write the information down in it. Keep your receipts in a separate file/envelope. There is nothing that says you must have them, and them alone do your maintenance, it is your right to choose the where part, and for your warranty's sake keep up with the when part.
I would have told them that the fuel filter was replaced 2K miles ago, and I would have questioned the need to 'flush' the system, that is not a standard part/practice when changing the fuel filter. In fact, I would have asked them why it was that they felt a flush of the system was necessary? Concerning the missing parts since they worked on your truck, I would be right back AT them questioning why they have not re-assembled things correctly? That to me is shoddy workmanship and poor quality mechanics. Did they give you your parts to keep safe until they finish the job? Or will you be buying new hardware when they finally complete the job? I would be in to the dealers owner and having a REAL conversation about the care and maintenance of my truck and what is not acceptable.
I would make sure that the service writer and mechanic knows that I already have the maintenance taken care of as part of my owner responsibility, and then remind them I was there for their part - the specific warranty work at hand. That type of statement alone should end his need to continue with the subject. If it doesn't, then I would pursue questioning him about what part of IT'S ALREADY TAKEN CARE OF he did not get. I had to remind my dealership that I was the person who actually owned the truck, not them, and I would make the decisions as to who would do what work and who would not. The real part is about getting it done in a timely manner consistent with a good maintenane schedule. I too would not let any of them wash my truck let alone work on it as I have already had my fill of their poor work and services. My dealer was on me about the need for an oil change, I looked at the guy and said "How do you know it needs one?" he said "Well, we have no records showing it has had one". I just laughed at him and said "Since when do you keep ALL the records regarding my truck and what has been done to it?" He stopped right there and did not persue it any further.
CD