Congrats. Before answering your question, I wanted to offer that most of my Chicago clients who get waitlisted at Booth or Kellogg get in if they withdraw from the waitlist at apply for part-time. Might consider applying PT at Booth.
With regards your question, are you sure that grades are what put you on the waitlist? Very likely, but I would get an outside perspective on that. The overriding goal is to demonstrate that you can handle the work. I would focus on the GMAT if there's any room for opportunity there. MBA math can form the basis of a secondary transcript, alternatively. I don't think taking a class or two is going to wash away an entire undergrad transcript, but good grades in quant classes would help if that's the problem. A longer-term solution would be the Harvard Strategic management certificate, comprised of six classes that you take in Boston. So that gives them a more robust feeling for your ability to handle academic coursework and also gives you exposure to in-person team work.
Often candidates get very caught up in trying to remedy their weaknesses in the application process, and forget to leverage their strengths, demonstrate their uniqueness, and showcase what they would bring to the class that no one else could. When you write your update letter, don't just focus on being good enough but exceptional- how you would add diversity to the class, and how that would enrich the MBA experience for your colleagues.