Will it count against me if I apply to a more popular college like Muir? Or do they not consider that when choosing applicants?
According to the UCSD website (and also what an admissions rep stated when I was attending a UCSD college visit), college choice does not affect admissions chances.
http://provost.ucsd.edu/colleges/
Basically, your choices are only considered if/when you are admitted to UCSD as a whole, and only for placement into a specific college. Hope that helped!