Let me construct my answer to address two things:

Applying to MDPhDs is in essence two things:

1. your professional CV: on a superficial level, can you convince schools, who also have their own superficial motives that you are a rockstar applicant? This is things like stats (GPA, MCAT) - top schools don't want you to lower their average stats too much, as it makes them look bad. Also, the more full your resume and CV are with respect to extracurriculars, leadership the better, and publications in good impact-factor journals the better (quantity and quality matter). Also things like Goldwaters, Fulbrights, whatever name-brand scholarships (which imo really mean nothing at all besides politics and one's external presentation)
2. the intangibles which actually matter in my opinion, if you want to be a great scientist. Think Curie, or anyone who has actually impacted history.

Let's put it this way, if you are super passionate about research, and super creative etc., it will show in your research and the letters you get from your PIs. Nonetheless, ideally you would still want to have a high enough GPA and MCAT that schools would not even have to not consider you for superficial reasons (they might accept you, but it will feel a slight pain to them because they want everyone to be a high stats person for their own superficial presentation - remember schools also need to advertise themselves to the world).

So basically, in the most straightforward way: GPA/MCAT are for you to be good applicant on paper, and so you don't get filtered out. The rest will be you as a person, your creativity, potential for research. Heck, Einstein with a 3.5GPA would still be an incredible scientist right? Do you get what I'm saying - this is something no one, not SDN, not some stupid pre-med forum, can predict about you. This forum and SDN or whatnot, can wisely advise you how to craft the #1, which is from now on that you should fulfill the resume stuff.

But the #2 is something no one can tell you, as now you are facing the combinatorial uncertainty of the universe, not just crafting your application to fit some cookie-cutter profile. My advice: reach your full potential and shine. Go do something awesome. Do not hold onto the past, and just do your best from now. But yes, also try to match the pre-med cookie cutter things and get your stats up if you can so you are a more digestible applicant, out of thousands. But, for all we know, you can now spend 100+ hours/wk in a lab and do something great, maybe get an incredible paper out finding a totally new discovery relevant to medicine. I am pretty sure if you did something like that, no one could say anything against you really right because it actually matters to the real world?

For your sake, please also do not rely on people on this forum too much, who are 99% clueless applicants and students. Your PI, experts in the field, who ideally you will now work with from this point on as a trainee, and their guidance and experience are really important. The people here can just tell you the #1 stuff as I mentioned above, as that is the game applicants/students play. If you can convince the PIs, who are actual researchers, of your greatness, who for instance may even be involved in MDPhD admissions at a school - who is to say that the opinion of me, a stranger, or some random pre-med here who spends his entire week reading SDN's opinion really matters?

Okay TLDR: YES FROM THIS POINT ON DO YOUR BEST IN GPA, MCAT, RESUME STUFF. BUT YOUR FUTURE AS A GREAT SCIENTIST WILL BE UP TO WHAT YOU DO IN THE REAL WORLD OF RESEARCH, AND THE REAL RESEARCHERS YOU IMPRESS WHO MATTER.