You will become way more aerobically fit, so don't worry about that. I had stomach issues when I started back as well and I found that I had to limit my eating to four hours before the run like you, and I had to make sure I drank more water during the day before the run. That seemed to clear my issues up. As far as running shoes, I would go to a specialty running store and have them look at your stride so they can get you in a pair of shoes that fit your running style.
Yeah, this is why my AM schedule is:
5:30a - wake up, sit on the can, put on clothes
6a - run
If i have a 5k or something, I will stay up a bit later the night before, and then wake up and go on an empty stomach. One of the dumber things I did was eat a banana before a 5k once. Don't do that. Just drink water, and don't be like the assholes who eat a Gu packet before a 5k. I would never laugh at somebody for being at a 5k and getting/staying healthy, but I still laugh on the inside when I see that.
This weekend I'm participating in my second 5k race. It's organised by a clothes detergent (MAS Color). There is no special prize for the winner, it's more about them throwing coloured powder at your white top to see how it ends up once the event has finished.
Here is a video of it.
http://www.youtube.com/watch?feature=player_embedded&v=pe3PltSMFho
Those always looked like fun. I'm doing a Color Run with my wife and son this summer. It's not something I'd do myself (it looks mostly female-oriented), but it's a nice change of pace. The Mud Runs look REALLY fun, but I'm afraid of injury.