This far into the school year there isn’t much you can do. I agree you should ask your guidance counselor to explain the scheduling conflict in the LOR.
In retrospect, it would appear you could have done a better job advocating for yourself. Perhaps gotten your parents involved. You might have asked which class was interfering so you could have made an informed decision to postpone that class to senior year so you could take APUSH and AP Lang. I would not have settled for “they’re full” as a reason without knowing how others got in ahead of you, despite you having a perfect GPA. Finally, you might have requested the school district pay for you to attend online AP classes for which you were qualified. They likely wouldn’t agree to this, but merely bringing it up, asking if escalating it to the school board might make a difference, would have gotten their attention, and signaled to them you weren’t going to be the pushover they could dismiss for their own convenience.
Hindsight is 20/20, but now you’re prepared when it comes time to pick classes for senior year.