11:15am cst - I called McGrath Honda again to schedule a service appointment. They transfered me to their offsite reservation center. This is the same reservation center which promised us a loaner one one occasion and we arrived at the dealership to find out there was no loaner available for us. I explained this to her and she assured me we would get a loaner this time.
I didn't want to take her word for it because of my previous experience so i called the dealership and spoke to Jeff (or Geoff, not sure). He said there shouldn't be a problem getting us a rental today at 4:30 when we came in.
4:30pm cst - Dropped into McGrath Honda and worked with a new service rep Matt. He played with the moonroof for about 15 minutes until he could replicate the issue on demand. It seems it is only having issues when the car is on. We moved on to the rear hatch issue and he was completely confused and baffled about that problem. He said they would look into it. Then i explained the issue with the brake pedal, and just like service rep J, he seemed to just dismiss the clicking noise and tried to explain that this noise is supposed to be there, even though we explained this noise was not occurring when we first bought it or in my mother-in-laws vehicle, or any other Pilot on the lot.
Matt was helpful and told us he would get us taken care of. Shortly after that we drove off in a Honda Accord as a loaner.
At this rate we would have driven all 10 models within the next few months. Hopefully it doesn't come to that.