Your grades will hurt you but your story and ECs show a lot of passion and are generally really good!
I recently spoke with a Stanford admissions officer who said if they just wanted grades and scores they could fill up their class 5 times over with perfect kids.
This is what you’re up against. My friend finaled at Intel science fair (2380 SAT and 4.8 GPA) and was deferred from Stanford EA. I’d say apply but don’t get your hopes up, Stanford admissions are a scary place but it’s not impossible.