Hey KevinT, you are way ahead of the game as the previous owner installed many of the preferred add-ons. Here is what I can offer:

2) What's under the cover in the right fairing, and why isn't there more storage there? - OEM Cruise control if you have it. Otherwise, coolant system cap and hoses. There is no room to add a pocket like on the left.
7) Is there an aftermarket rear brake pedal in black? - Not that I am aware of. Easier to have yours powder coated.
8) Are the stock stereo speakers silver in the middle? Not sure if mine are stock or aftermarket. - OEM speakers for my '13 were solid black, no silver center.
9) What are the best after market slip-on mufflers to use with Torq Loops? Man, you will get so many answers for this one. lol I do not have Loops but I chose Bassani and love the sound.