I'm not in an MD/PhD program (yet, hopefully I will be soon.) But here are some of my "observations"
1. This subforum is doesn't get the same traffic as many of the other forums, so give an thread ample time before worrying if no one will respond. I have often posted in here and waited upwards of 2-3 days before a response tendered back to me.
2. Don't look at the stats of those in the acceptance/wait-list thread. I personally believe that SDN membership is very auto-selective; only those who are extremely motivated (most of the applicants in this subforum) actually visit this site or those who are not very competitive(me, for instance). There hardly seems to be a middle ground, so don't worry about others stats too much.
3. From my observation, it seems like the world will not be over if you don't get into one of NIH funded MSTP's. There are tons of programs that are self-funded (I'm only talking about those that offer a full ride and stipend) that send their MD/PhDs on to very competitive fields at top 10 academic centers. Also, it seems like most residency programs don't care too much about the PhD, so no matter where you go you'll still need to bust your ass and do well on Step1 and get honors during your clinical years.
My point is, even going to a less renowned MD/PhD program (Oklahoma, Ohio State, Jefferson, etc.,) doesn't auto-select you out of competitive programs. Just take a look in here and see all the threads of MD/PhD's who worry if they'll match ANYWHERE due to a low step1/preclinical grades/whatever. You will have to work hard anywhere, and us uncompetitive people should be thankful for that. 🙂
3. If you have a 3.5 there is a good chance you'll be compeitive somewhere, but you won't get in to multiple "top-10" schools. A 3.5 probably doesn't even limit you to none, as there are a few people in this subforum who had around that and go into great schools. There are a pretty decent smattering of schools outside of NIH funded programs, so look at those.
4. Your MCAT does seem a tad low in combination with your GPA. Do you plan to retake?
To end, once again, consider I'm an applicant this cycle like you, just trying to help. 🙂 I'm sure some of the stuff I've said could be wrong, so take it what it is worth.