@impressivemediocrity, congratulations! Your name beguiles your reality :-). In general most of top schools, including some bs md programs do ask for the 1st semester or equivalent grades of senior year too. But they also understand that this is a stressful period to most, due to application process, standardized tests, challenging senior year course work (some high schools are not so willing to let the kids take too many APs prior to junior or senior years) etc.
Also a course like AP literature can be very challenging grades wise and also depends a lot on the toughness of the teacher. I am sure the admissions folks know and understand all that. So you don't have to worry. Just focus on your studies and continue to impress :-). But in the worst case if certain school / program does care and holds it against you, then who cares? It may not be even worth attending such a program with such rigid selection frame work, mindset and criteria. Good luck with everything.
Also wanted to add, there is no consistent AP policy across the board. Have personally come across kids with not so good AP scores (3s) still getting called for interviews and even offered admissions. So let AP scores not demotivate anyone. Its good to have as close to perfect scores as possible, but not a deal breaker otherwise. If the programs are picky and choosy they will let it known upfront one way or other, like Northwestern for example where they will review the applicant's entire academic track before even deciding whether or not to send the application link. Also you can check with the admission counselors where and when you visit.
Let me also add, apart from the scores in them, what APs taken also may be looked into. BCPM may weigh in the most - Biology, Chemistry, Math (Calc) especially followed by Physics (preferably C level, Calc based).
Went through some profiles where the kids were going all over the place with the APs, it may sound to the admissions folks of these programs that they were doing it more for the number of APs under their belts, to impress them, and not out of real interest, which may prove counter productive.
@njdesimom, As far as I understand, you can apply to one, some or all the feeder schools and depending on whether or not you get the interview calls, if any, and if selected, the applicant can opt which feeder school to attend. The feeder schools have their own policies of who to forward for the medical school consideration. Example that may be particularly relevant in your case, NJMS --> feeder schools: NJIT, Rutgers, TCNJ, Stevens, ..... Generally people apply to couple of feeder schools where they think they have best shot at getting forwarded for the medical school consideration. Also, if selected, it may make a lot of sense to consider which of the feeder schools are relatively relaxed and which are stringent as far as medical school matriculation is concerned (primarily, GPA, MCAT score, grade deflation at the particular school etc)