Title sums up my dilemma pretty well. Details: I missed around 230 classes, so almost 40 days of school, in junior year due to sickness. I have a 504 plan for autoimmune&chronic diseases, and I also did (mostly) fine last year, passed all my classes and whatnot. I want to seem ready for college, so I feel that having those absences on my record makes me look shady and unprofessional. What is the best way to clarify my absences with the colleges I am applying to?
Your guidance counselor, not you, will explain that to the college.
Does your transcript list days absent? If so, then have your GC mention that you had an illness that caused a lot of absences that year.
Agree, this infomration is best coming from your guidance counselor – you can ask him/her to include it in the LOR sent to colleges. This way it comes off as independently verified information instead of an applicant trying to make some kind of an excuse.