There is much consistency in your career as a student and physicist, which will look good to the adcoms. It's also unique to come from a non-feeder industry (such as banking, finance or business). For these reasons, I think you'd have a shot at all your target programs. Don't worry about GPA below 3.0--you'll get points for a tough major and you have a master's degree, so I doubt they will have concerns over your ability to handle the MBA. PT programs are more lenient anyway. Let us know if we can help you prepare your applications.
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