Would it effect when I'd be able to apply for college if I retook two classes senior year?

You should talk with your school counselor with this. It sounds like you could be successful, but it all depends on what colleges you're going to. Some have strict rules when it comes to what classes they expect their incoming students to have taken and passed. I even know some colleges that are ok with 3 yrs of science and math. It all depends. But I definitely encourage you to talk with the school counselor to have everything straight before you start applying to colleges.