MCAT too low for great MSTP?

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Assuming you are applying next cycle:

Don't retake. You have a strong app for top- and mid-tier MSTPs. Anything is possible, and the general advice applies (apply broadly and early) but I'd be surprised if you didn't get a handful of top-tier MSTP interviews and an acceptance. I'd advise option (2).

If you makes it feel any better, I have several classmates that matriculated to our top-tier MSTP with similar stats.
 
Don't retake. 519 is good enough to be competitive for every program. Research experience will be the most important component in differentiating yourself from others. Some top MSTPs have medians above 520 (Hopkins, WashU come to mind) but that doesn't mean that you need a better score to be competitive for those programs...