Independent Studies Not Listed on Transcript

I got my schedule back for Senior year and there were multiple conflicts with my core classes. I signed up for AP Chem, AP Physics C, AP Lit, AP Music Theory, and AP Calculus BC. AP Physics C was immediately cancelled as only three students signed up and my other courses were only offered during 4th pd Choir (really involved/one of my main ECs, so non-negotiable) and/ or 5th pd. After deciding to drop AP Music Theory, I only had space for either AP Chem or Calc BC (took Stats last year bc of same conflict). I needed a 4th year science credit to graduate, so I ultimately decided to go with Chem. Calc AB is offered the same periods as BC, so I had little choice there. The local CC wasn’t an option either bc Calc and Chem aren’t approved DC courses.

I’m currently signed up as a teacher’s aide for two class periods where I would use the time to go through an online Physics C(Mech + E/M) course and Calculus BC. School policy won’t allow me to get any credit. My only worry is that as my independent study courses will appear only as free periods, it looks as though I opted to take only two academic courses: AP Lit and AP Chem. I’m aware of the additional info section on college apps, but I’m concerned that schools will assume I am slacking off in a major way Senior year before reading the rest of my application. Will my independent studies have a negative effect on my application and is there anything else I can/should do? I plan on applying to UT Austin Honors(in-state), Pomona, MIT, Yale, and Stanford this Fall as a CS+Sociology major.

Senior Year Transcript:
H Symphony Orchestra
H A Cappella Choir
H Science and Engineering Mentorship
AP Literature
AP Chemistry
Teacher’s Aide 1
Teacher’s AIde 2

I’ve also already finished three years of foreign language and all SS courses except AP Psych and AP Euro.

If the school isn’t giving you credit, it will not appear on your transcript. If you take the AP test for Physics and Calc, th colleges you apply to will see those, but it will be long after the admissions decisions.

I would ask your guidance counselor to mention your scheduling conflicts and the online classes you are taking in his/her recommendation.