I am a Junior in high school taking Pre-Calculus and am taking AP Calculus AB senior year, will this affect my STEM college admission?

Self-study AP CS principles or a college CS course that inspired it (e.g. https://cs10.org ) out of interest (you probably want to skip any programming stuff that you already know from CS A), not for its AP credit, which is not generally very useful in terms of subject credit or advanced placement, especially if you already have AP credit for CS A. AP CS principles is more of a broad overview of the subject, and is not a subset of CS A, although it is generally considered less difficult than CS A.

AP calculus AB in high school is fine for applying to any major in any US university as a frosh.