1. 87 octane minimum. My truck didn't like 87 or 89 so it gets 91 all the time.
2. Modding is fun.
3. I prefer the Magnaflow sound but I can't pick an exhaust for ya. You have to listen to some to see what sounds good to you. Remember, the longer the muffler case, the quieter the muffler. Go to the 5.7L Hemi Exhaust mods section. Lots of info there on exhausts.
4. No opinion on flexible or folding tonneau covers. I've only had the hardshell type.
5. I prefer the AFE units but before you buy, check out this thread:
6. I've leveled three trucks and lifted two. Daystar and Hell Bent Steel make good ones. I went with a 2" kit all three times and it was just right.
7. Since your 2011 truck's software has been encrypted, getting a tune is problematic. I have a 2006 Chrysler SRT8 and this 07 Hemi truck. Both have DiabloSport Predator programmers on them and the SRT has a custom tune. This will void your warranty but the results are awesome so you have to make a value decision there.
Good luck and have fun reading the forum. There is a huge amount of info here on a myriad of subjects.