I have a roughly similar situation. I dropped off my undergrad once, and started again. My undergrad GPA is around 3.0, second upper class , which is bad for a PhD applicant . I got average GRE, and a good masters degree, by the way.
Although it is not stated, but I believe my GPA hurt my chances quite bad.
IMO, the best like MIT, Stan, Berk, etc may be very difficult. But you have good chance at the second best like UIUC, Austin, UMich, etc.
By the way GPA is only one aspect of your application consisting of many, such as research, LOR, essays, and so.
All the best my friend.