the CSU Mentor application requires that I have two semesters of visual/performing arts. I have one semester of drama. Is it possible that they would overlook this, seeing that I have filled my schedule with honors science/math classes and other weighted classes? Also, I’ve played guitar for 5 year, but not taken any class in instrumental music, would this help?
If it does, I still don’t know what to do because the application won’t be marked complete until I have 2 semesters of arts.
It is a UC/CSU requirement for 2 semesters of a VPA. If you do not meet the requirements, your application will not be considered. I suggest you look into taking a community college class or an on-line course to fulfill your 2nd semester. Guitar lessons will not count. Any instrumental class needs to be UC/CSU approved.
Doesn’t the application count courses that are to be taken this year? Can you alter your schedule to include a vpa class next semester? Believe me if you are otherwise taking a heavy load of stem courses it will not hurt you to take a break and train the other side of your brain 
I’d recommend talking to your guidance counselor and seeing if you can get approved right quick for something in the visual or performing arts.
The UC application will ask for classes in progress and planned in your Senior year. Definitely drop one of your STEM classes in exchange for a VPA course. If you take a VPA course at a community college, 1 semester will equal a year course.
Don’t take an online class - the UC’s do not approve online VPA courses. http://www.ucop.edu/agguide/a-g-requirements/f-visual-performing-arts/faq/index.html
You need to take one more semester of VPA. Any community college class will be good - even a Winter quarter class will do the trick.