Yeah, I got in this cycle with those kinds of grades (lower cGPA though). I had really great LoRs, extracurriculars, and experience to make me look more appealing than my grades did, though. I got a D in organic II the first time I took it and was fine with my retake.
your title and contents are confusing lol...so at the end, you passed your orgo. Yes I had one F in Bio and one D in Cell Bio..then repeated. I got accepted to all schools that I went for interview still.
You have a 3.5 GPA and you re-took org chem and got an A and are freaking out about getting in?????????????????
If your GPA is a 3.5 you have a great chance at getting in, no need to be scared (unless of course you got Cs in every pre-req class, then it may be a little more difficult).