12:45pm cst - Just received a call from Matt at McGrath Honda. Here is what he had to say on the three issues:
Moonroof - They took a look last night and reprogrammed it so it would close. They are going to have the technician go through the cycle of testing again that Matt performed when we dropped it off (open and closing while car is off, on, in park, and in gear).
Rear Hatch - They can obviously tell the hatch is not aligned properly. They ordered new parts and will replace the broken piece and re-align the hatch properly.
Brake pedal - The technician compared the noise to another Pilot and confirmed ours was making noise. He lubricated the nylon strip and according to Matt "you will still hear it but it is 30 million times quieter."
He hopes to call us tomorrow to pick up the car, but not sure yet when the parts will arrive.