I am very sorry that you have been dealing with health issues. Stanford has the lowest acceptance rate in the country. Your test scores and GPA are subpar. Stanford has no way of knowing how much better you would fared (if at all) if you weren’t dealing with your health problems. You’re asking them to speculate on what type of student you could have been and will be when they have thousands upon thousands of applicants with stellar grades, test scores and EC’s that they can select and feel more certain about their choice.
I wouldn’t apply early if I were you just because you think your chances are better. The early applicant pool is extremely strong and contains many kids with hooks. You should use your early option for a cool where you have a more realistic chance of being accepted.