I would switch out a few Mstp's on your list for a few more non-mstp funded MDPhD programs. As much as people can be understanding to your story, they still have to report incoming GPAs. Whatever you do, pick your schools and get that app sent out ASAP. Don't wait any longer. Do you have any secondaries written?
Thanks for your advice. I'll look into some of the non-MSTP programs as well. I have already submitted my primary application about a month ago, I was just waiting to get my MCAT scores before designating schools!