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Have you also considered applying broadly?
I'd suggest that adding some DO schools should be part of your plan for "applying broadly."
And I do think you'll be disadvantaged to have your clinical experience acquired over the last 6 months. About 1.5 years is average, and a year is the least that most successful applicants have. It might help that the shadowing occurred awhile back as a demonstration that you were thinking of a potential medical career for a longer time. But the flurry of activity does suggest a last minute decision. If you are close to a school's expectations, then they might regard update letters giving additional hours of involvement.
That you got some clinical time in last summer helps.
It sounds like you were in a Special Masters Program. If so, that completely changes your application dynamics, especially as you beat the 3.5+ expectation for what is considered to be doing well.
An SMP GPA can override a low undergrad GPA, which is not true of a traditional masters degree. And your 3.5+ GPA passes a meaninful threshold.
Did you start your summer's clinical experience gig before you applied so that it's on your application? If not, maybe send a separate letter after you've submitted your Secondary to each school telling them about it (if there is no Secondary essay where it can be mentioned). Do so again in mid fall and again at the end of the fall semester early December since you aren't waiting for grades to come out). Etc. I agree this activity should be continued throughout the application season. The letters can be used to mention any other factor significant to your application as well.