Thank you so much for your quick reply! It has helped me a lot and I feel a lot better now.
Just to reiterate, they WILL look at other criterion and not just solely base it off my GPA? I will definitely try and sell my SOP using the research angle as this is what I intend to do.
Thank you for letting me know of other good schools for CV and I will definitely apply to them. In your opinion, I do have a chance to get accepted in at least one of the schools you mentioned? Also, will I be competing with Master's students for a PhD admission or will they consider jumping from BS to PhD a separate track? If the former, then do you think having 3 publications is good enough?