I might be totally wrong, but from the details you’ve given there’s a fair chance we went/go to the same high school, and I was the only one from that school who got into MIT last year, so hopefully this will help you.
- The class rank issue. I had the same issue! Just ask your counselor to use the weighted rank instead of unweighted. Weighted I was first, unweighted I was barely in the top 10%. It definitely didn't stop me from getting in to schools.
- Don't know how much sports will help you; last year there was a kid in my grade who was recruited for football at MIT and still didn't get in.
- The research and publication won't help that much unless you also submitted to contests like STS or Siemens and was recognized.
- MIT barely takes kids from the school district, let alone the school. Of course, this is me guessing about your whereabouts, so if you're not in the Portland Metro area, you can ignore this.
Good luck!