Welcome and Congrats!
The transmission noise is normal and has been discussed extensively. Just do a search and you will find all the information your looking for.
Rust will only happen when nothing is protecting the metal, so unless its more of a chip than a scratch, you don't have to worry. The paint doesn't look all that bad and doesn't need a re-paint just by looking at the pictures. First I would try having it professionally polished, not the dealer. It doesn't look like it went below the clearcoat, so a fine cut polish could possibly remove it. Hand polishing might not be enough, so have a pro use a machine polisher. You could also ask the dealer to offset the cost.
The detailer at most dealerships aren't exactly the most skilled in detailing, so I would try and stay away from having them do this. If you take a picture of the paint with a camera (flash on) or look at the paint in direct sunlight, I guarantee there are swirls from the first detail when you picked up the car from the dealer.
Also, our paint is on the soft side so make sure you take any bird droppings, tree sap, etc. from the paint right away, especially since your car is Black. Otherwise, you will see marks from the "acid" start to eat away at the clearcoat. It can be removed, but only with polishing, so never let it sit.
If you want to try to do it yourself, Meguiars & Adam's Polishes (forum sponsor) have kits available that are better than the most off the shelf auto store products.
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[09][MB][6-Spd MT][Touring][Stillen Gen III][K&N][Borla CBE][Evo-R]
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