2. A STS is a great idea. I have the factory one and I like it. Well worth the money - just be sure to get the bushings as well. Again, you can go aftermarket if you wish.
3. The 5-door has more usable storage space, especially once the seats drop. Looks is up to the owner, though I like the 5DR better - fits the style well.
4. Don't know - haven't really seen anyone with them.
5. Stock has a nice sound straight up, and the SPT is a bit meaner sounding. If you plan on modding later you may want to think about staying stock so you can add a TBE later without losing money on the SPT.
6. I ordered with the dimming mirror, STS, and armrest extension. Each was a great choice. Sometimes wish I'd gone for the SPT exhaust, but the cost wasn't in my plans at the time so I'll live. The stock sound is solid.
Have fun and good luck with the process.