I can answer some of this.
My chair made a creaking and popping noise when I had the lumbar set at a specific spot. One little tiny bit less or more, and all is well. Don't be afraid to try that.
The transmission clunk is a warranty item, and should be given to a dealer to figure out. When it doubt you can always pull the battery terminal, let the system reset, and then relearn.
I'd like a picture of the leather in the chair. If you have the Napa leather group, it should be full-aniline leather and therefore and cracking or other aging should be a natural look thing, and there should be no chipping or flaking of the top coat because there is no top coat in this type of leather, and a leather cleaning and treatment should improve the look. If it is semi-aniline (non-Napa type), then warranty should be good for a while on this item, and would cover a replacement seat cover and the labor if it is a defect.
The part I know about directly is how GAP and other products work from the finance dept. You can either trade/sell, get the proof of payoff letter and walk in to the dealer and get a check cut to you (in usually 4-6 weeks), OR you can ask for those to be returned now and the money difference will reflect in your principle of your loan.
For Nevada, there is a tax credit of the difference. Also keep in mind, you want to claim taxes on your IRS tax return as a tax-deductible thing, which should be universally applicable across all states.
I'd recommend, as badass and expensive as this car is, give the dealer (or maybe a second one if this one can't do the job) a chance.
Please upload pics of your concerned seat parts when you can