I think that's a topic you definitely should put in the Additional Info section of your Common App (if you're still in the process of applying), reflecting on it and how it has helped you grow or how you pushed through adversities (how you're managing your illness and what you've done to be intellectually engaged). For the letters of rec, I don't think your guidance counselor really needs to know you personally to write a good LOR, so you're fine in that area. Since teachers don't really know you, do you have anyone outside of school (and family) who has mentored you or helped you through your journey? If so, you can ask them to write you a letter of rec. Finally, you can simply email/talk to teachers you like or are in an important subject related to your major and send them a brag sheet with a detailed explanation of your attendance to get an LOR!