What to do with clearly not good enough profile

[Linda Cai]

I am currently CS and Math double major in UIUC. I am planning to apply for Theoretical Computer Science thesis master/phd and want to experience a new school. 

Due to the fact that I transferred into CS my sophomore year (was a business student), it took me a long time to form my life objective in the new department/major. Plus I didn't use my junior year wisely (spent majority of first semester trying to find an internship and let classes take away too much time from my research). Now I am thinking that it is impossible for me to get in anywhere except UIUC. 

Goals: Stanford(master), Mit(master), Cornell(phd because their master sucks), Toronto(master), UIUC(master)

Credentials:

GRE: 160 + 170 writing 4.5

GPA: 3.97 

Recommendations: One from my thesis advisor(on constrained least square, still on going), another one from my other research on earthquake simulation. Potentially one from my algorithm II professor where I got top 5 in the class. 

Research:

I have been a research assistant to my thesis advisor for 1.5 years. However 1 year I was programming educational modules for my professor, which visualizes different numerical methods. Obviously result in no publication.

My thesis is a comparison study of ways to solve constrained least square(possibly do some theoretical analysis), and my literature review just got submitted. Advisor just let me do whatever I want to do so I really need to push myself on this project. 

My other research is on earthquake simulation. Last semester I pretty much optimized the code for the algorithm my grad student wrote. This semester I will be more involved in developing algorithms for different earthquake scenarios. They said next publication would have my name on it, probably not in time for grad school app. 

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Any suggestions on what I can do to improve my application/portray it in a more positive light?