The U of M admits students on a rolling basis so it’s generally better to apply sooner rather than later as spots begin filling up. If you feel confident that you can adequately explain the health issues you dealt with, I would recommend applying by the first deadline as your grades from the periods you weren’t dealing with your health issues are a lot stronger. The U should understand that your freshman year and junior year fourth quarter grades more accurately reflect your academic ability.
You can also check out the profile for admitted CSOM freshmen here: