Hey lookstock...nice choice on the DNX7100...I still love it.
1. As far as upgrading the stock system, you can't. It's all integrated together and if you swap out some components, you'll need to swap out the entire system including wiring.
2. See #1.
3. Yes, you will lose the center speaker....if you get some good aftermarket speakers for the doors, you won't miss it at all. I don't!
As far as the menus go...they are great. It's a very visual display and I didn't have any problems navigating the menus. I did quite a bit of research before settling on the DNX7100 and I'm VERY happy with my decision...the sound is awesome, the display works great....try watching the movie "300" sometime...it's amazing on that tiny display! And the Garmin Nav is seemless.
Fyi...if you've read my other post regarding the unit's installation, you know that it sounded pretty bad (to me) using the METRA TYTO-01 adapter to the OEM 10 speaker system. You may have better luck.
Good luck and seriously consider swapping out the entire system. I know it's more $$ but in the end you will be much happier.