Hi and thanks for posting...
You have some competitive (!) schools on that list, and some challenging issues you've mentioned, but you've also shown a maturity and self-awareness of past weaknesses and challenges and ways you've overcome them that I think will serve you well as you put together your application, essays, and interviews.
You are correct that your masters degree with the high GPA will help out that undergrad GPA, and you would likely use the optional essay to explain more about your undergrad situation.
You should as you probably know aim for over 700 on the GMAT for those top programs, and yes HBS and Wharton will be a stretch. There's not too much more you can do at this point unless you take on any particularly interesting projects/accomplishments at work between now and when you apply, or get involved in a community activity... with your masters degree it's less pressing to say, take some additional coursework. So I'd focus on the things you CAN affect-- your GMAT and your essays! Don't underestimate the importance of the essays, nor the time it takes to really create strong essays.
Wishing you the best!
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