Got my first mustang today..02..basic questions

[blue00gt]

Congrats on your new stang!
Unless you have a timing adjuster or run forced induction there is no reason to use anything more than 87 octane. Higher octane gas just burns slower (takes more temperature and pressure to ignite), so if you don't need it there is no point in paying more for it.
Aftermarket cold air kits don't add much power, so unless you want it for the looks you are better off just ripping out your intake silencer and dropping in a K&N. They may hassle your for a CAI on warranty, but they won't for a drop-in K&N.
Basically anything more than a K&N and a catback is going to depend on the delaership whether they want to hassle you about the warranty or not. Other than that you can try things that they aren't as likely to notice.
Peak power on a stock 99+ GT comes at 5250 rpm.