My questions to you would be:
1. Am I competitive at HBS, MIT, Kellogg, Michigan, Texas, Chicago, Wharton?
Yes you sound like a competitive candidate with a very interesting background -- the essay award stuck out given your profile.
2. What part of my profile could I improve this late in the game? Will last minute community service look contrived?
Sounds like you need to spend more time thnking about your career goals. I think the combination of your interest in martial arts and extracurricular open source activities can serve as a proxy for com. service. I wouldn't just pick up some random activity now to check the box. Back to career goals: Really spend some time thinking about what really interests you -- what you're passionate about and build a career around it. You've listed some obvious paths (consultant / entrepreneur), but if you decide to focus on those, make sure that you have some ideas that you want to lay out and don't just present those paths generically.
3. I've heard a rumor that schools don't like you if you did undergrad there, because of "lack of diversity." Since I did my undergrad at Michigan, should I even apply there?
There's a bit of truth to that rumor. If you were a BBA at the school (say Michigan or Wharton) they might not be super excited about it, because the thought is that you would find the MBA program to be somewhat redundant. This doesn't apply to your case though, so I wouldn't shy away from Michigan -- even though I'm a Spartan, I won't lie to you.
4. What's the probability of merit-based scholarships for my profile? Would it be totally unqualified to expect any? Should I look for this only from the trans-elites?
Well, HBS has no such thing. For the other schools, it is a possibility. Probably not full-ride, but there's a chance that they'll throw some dollars at you.
5. What other schools would you recommend?
I was surprised that there is little to no west coast representation. I was surprised that Andersen, Haas, and especially Stanford didn't replace some of your other picks.
6. If I were to pitch myself as all-entrepeneurial, would I have a better shot at getting in? Do schools pick and choose candidates based on intended concentration?
Maybe -- honestly I'd have to know a lot more about you to give you a conclusive answer. In general, true-entreprenuers fair well given their breadth of experience and the fact that it's not the 1000th consultant/i-banker to apply. But people who "fake the funk" might get burned. Based on the little I've read, it sounds like a good position for you though.
No -- schools don't really choose based on intended concentration.