May additional time in college harm my chances of going to grad school?
Taking a long time to complete one degree can be a bit of a red flag in US graduate admissions. However, this does not apply in your case, because you will have three separate degrees. The fact that you have transferred from one school to another also mitigates the lengthier time you've spent in those study programs.

If you hadn't done this "master of advanced studies," spending 7.5 years as an undergraduate would probably not be looked on too favorably. But in your specific circumstance, it's not as bad as it looks at first blush.

There might be a question, however, about why you want to do EECS at the graduate level, given that your master's degree would be in a math-related field. But that would be up to you to explain in any case as part of your statement of purpose.