@supercilious, congratulations on your achievements to date and on your clear focus.
It’s too early to say with much certainty, but you seem to be making a splendid start.  I’ll address Duke since it is one of the 3 schools that you listed, since its probably intermediate between Yale and Williams in terms of admissions difficulty (though all 3 are tough), and since the Admissions Office has been fairly open about what they look for.
Duke screens all applicants on 6 factors, which they explicitly emphasize on their website: GPA, test scores, curricular rigor, ECs, essays, and recommendations.  According to results made public under federal FERPA law, they do a quick screen of these 6 factors for each applicant ranking each from 1 (worst) to 5 (best), and reject about 50% of all applicants based on this screen.
http://www.dukechronicle.com/articles/2015/03/23/ferpa-request-gives-inside-look-duke-admissions-process#.Vamw7WA9b8k
Your essays and recommendations obviously can’t be evaluated at this juncture.  Given your scholastic and latin awards, I would expect you to have both the subject matter and the writing skills to put together an outstanding essay.
Your SAT I score of 2380 and Sat II Biology score of 780 are fine.  The 25-75% SAT range for Duke for the class of 2017 was 2090-2360, so you are in great shape.  I wouldn’t bother to retake those exams, or add ACTs.  APs are optional - they don’t hurt, but they will count more for placement than anything else.  If you are in the top 2% of your class rank then your GPA should be fine as well.
That leaves curricular rigor and ECs.  You want to make sure that your curriculum gets checked off as “most rigorous” by your GC, and is within the high end of what your school allows.  As for your ECs, you are doing a great job focusing in the humanities and writing, with publication and awards showing strong achievement and commitment.  Great job.  I wouldn’t worry in the least about “starting something” to show “leadership”.  You’re doing just fine.
All of the schools you’ve listed are tough, but there’s nothing you’ve done so far that limits your chances.  As an Asian male with an outstanding humanities background and focus, you are probably going to stand out.  Just keep up the good work for now.