Some general recommendations (please note that each person is different and there are exceptions to every application due to varying circumstances - I, for one, am an outlier so you never know - I recommend taking everything with lots of grains of salt and learn as much as you can from multiple trustworthy fonts of information to make you final informed decision):
1a) Reframe your 2x Ws as you being wise enough to know you misjudged something for that semester and avoided a permanent GPA issue
1b) Keep an easily accessible journal entry about your reasonings for dropping those courses so you can articulate that during your secondary applications and/or interviews - they might have questions specifically asking you about them and a coherent narrative wherein you don't shift blame but also have a good reason (that you also have tangible learning outcomes to speak about) will be very, very helpful!
2) Take the MCAT extremely seriously - although I personally do not think the majority of the content is particularly relevant to what we study in med school, the habits formed by studying in earnest are imo key to the foundation of medical school study success. Your score on the exam is a decent indicator of your ability to sustain the type of studying needed for medical school and will be a key performance indicator for ad comms.
3) Try your absolute hardest to boost that sGPA - because of the One Big Beautiful Bill Act (OBBBA), unless you are wealthy I think an SMP or even DIY postbacc will cost you big in the long run (due to the cap in financial aid we are spiraling into) since you might *have* to get a 10-15% loan for a portion of that graduate level work... I am sorry you cannot fully take advantage of those if you will need it like we have been able to up to now (I did a DIY postbacc, funded by student loans, and grew *a lot* from it). With that, do all you can to not be in that situation and strive to bump up the GPA with high performance in future classes.
4a) Not a popular opinion, and even less so now due to OBBBA, but still an option - there are different pathways to becoming a physician-scientist: you can do a fellowship post-residency (no separate degree added, but you do get research training to be an independent clinician-researcher); you can pursue one of the few remaining residencies that grant a PhD (dunno if there even *are* any left - I am old); you can do a DIY wherein you take an approved leave of absence after year 2 of medical school and pursue the PhD on your own; you can pursue a PhD before medical school; if you only get into a single degree program and don't want to extend your now expensive student loans by forcing a PhD during medical school, and you years later still feel the itch to get that PhD training... you *can* pursue it after becoming an attending (I have met a few who have done that) depending on your workflow and if the program will work with whatever FTEs you can negotiate during your training.
4b) Obviously the traditional dual degree pathway is optimal and what you need to shoot for if you're committing to this route - I am not saying to make any of these other options your #1 choice, only saying there *are* other options if push comes to shove and you really want to become a physician-scientist.
5) Finally, do not get overly discouraged upon approaching the application. MSAR doesn't show the bottom % of people accepted into specific programs and you never know what the "real" lowest stat a program will accept - your stats are still good and commendable and it is obvious you have worked really hard to this point! Online reporting can make it sound like only the top 1% of students get into these (essentially) full ride scholarship training programs, but that isn't the case. Every year we see people with either a sub 3.0 GPA or sub 500 MCAT get in (doubt any with *both* but you never know!) - you are nowhere near that, so please don't feel down in the dumps! 😀 You have a lot of time left and already have a strong start! You've got this!
I would also recommend signing up for the American Physician Scientists Association's (APSA) mentorship program, as well as looking at SDN's Dr. Emil Chuck's "Becoming a Student Doctor" workshop.
You've got this!