What can I do to maximize my chances of getting into a CS PhD program if I switched to a CS major during my junior year? I was a business student for my first two years of undergrad but then switched to computer science. I took classes over the summer before my junior year at another school. During my junior year (which I am in now) I am/have taken 7 CS/upper level math courses. During the summer I am doing research and taking non-cs/(core classes for my undergrad curriculum) so that I can take only CS classes senior year. Fall semester of senior year I plan on doing an undergraduate thesis class and take two grad classes, along with another course. 

How bad is it for my application if I only have my junior year and first semester of senior year for the admissions committee to review. 

I have pretty good grades in my cs/math classes post sophomore year (A's/A-). I plan on having two good recs at least. My main concern is the lack of semesters for the admissions committee to judge me on.
The first two years of undergrad in the US are mostly general education classes anyway, so I wouldn't worry about it. It is common to switch majors.

You seem like you are in great standings. You've taken a fair number of CS classes, received good grades, and will have two good letters. On top of that you'll have research experience and plan to take a few graduate courses.

From the little info you've provided, you seem like you are well on track!