Hm. good questions.
- Yes your grades are taken into consideration. Often times, your Grades, PS, MCAT and ECs are really the only thing that schools have so they can know a little bit about you. 3.1 is a little low for most schools as generally you want to aim for a 3.5 or better to be considered competitive.
- This can be tough one. My question for you would be if you are actually interested in medicine and why. More specifically, if I were in an admission committee, I'd want to know why you switched from ministry to medicine. They're both very similar fields: lots of interaction with diverse groups of people, altruistic, and a opportunity to make a difference in other people's lives. However, medicine is far more bureaucratic and, for some people, extremely souless and demoralizing.
If I were on an adcom, (And I'm not btw) I'd want to know that you can handle the worst aspects of medicine and that's okay with you. It seems like you've had some more research experience working in the Eye and Molecular Bio areas of Vandy. That's all well and good but I'd be concerned whether or not you could handle the stress, hard work and bad situations that doctors are sometimes, often exposed to in a clinical setting. For example, most patients nowadays can be extremely belligerent and may actually not want your help.
The best way to tackle this problem is lots of work in diverse clinical setting. Go out and volunteer, become an EMT, etc and really get exposed to the environment. Seriously commit to that work for about a year. If you volunteer for about 150+ hours that would show most Adcoms that you know what you're getting into, you're serious about doing it.
In addition to that, research is always viewed favorably by most top schools and so is teaching. Often times, doctors have to teach patients some very advanced concepts in a way that the patient can understand. I'd also say your religious background would be advantageous.
Hope this helps.