Why do you think you were unsuccessful in MSTP applications? My experience is generally that internal applicants are judged as whether they would be acceptable candidates externally. However, this can vary from program to program.
Generally, get in touch with the MD/PhD program there and make it clear that you intend to apply internally. Get advice from them about whether you'd be competitive and what to do to strengthen your application.
Also, see if they have any laboratories they can pair you with to volunteer before M1 and between M1-M2. Have some in mind as well that fit your research interests, and you can ask if they have experience with those labs and use that to guide which ones you contact first to volunteer.
If you can spend time during M1 that's also great, but you do need to pass med school.
Worst case, my advice is not to bother with an unfunded PhD, but try to find ways to stay involved in research that are funded including year out programs and research residency programs. You may be able to pick up a PhD during residency or get enough research experience to become a physician-scientist without a true PhD. Of course, if you're from a well-off family, this advice may not apply to you and you could take a leave of absence for the PhD if you really want.
