Will these "red flags" hold me back from top schools?

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Gonna depend on your mcat; a 520+ will keep you in the conversation provided the rest of the app is up to par
T10s are a crapshoot to begin with. Aside from your grades & hopefully stellar MCAT (as mentioned above), you will also need stellar ECs. Then start sprinkling in luck.
 
Haven't taken MCAT, aiming for top 10. Classic.

If your GPA is above their 10th percentile, it is serviceable. But take the exam first - if your result is high, you have a shot (albeit low, like everyone else due to competition). If score is low, it will be highly improbable.
 
It sounds like all told ur only setback is the freshman year 3.2 and besides that you have 3.8 or better so your GpA is probably sitting at like 3.8 ish? Nobody will care about this. But without an mcat score or ECs or any other context its impossible to “chance” you.
 
sGPA is the #1 academic factor followed by the MCAT that is considered by admissions according to aamc and yours is not within 10th percentile for the top 10s according to MSAR. Unless you manage some insane MCAT score, it will be extremely difficult disregarding some sort of monumental ECs or research. It's like the equivalent of applying with a 512 MCAT or something to these schools...even if your GPA is mega high it will still be really hard and definitely not something you should bet on.
 
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