go_stats_or_go_home

@CB20 I emailed UCLA and UC Davis over last weekend, because I haven't heard back; apparently my applications are still under consideration. I'm guessing I'm either in consideration for another wave of acceptances, or an unofficial waiting list. 

With your GPA being so low, I don't think it's worth it for you to apply to Stanford, Berkeley, Chicago, CMU, Duke and Columbia. Those are the top programs and have tons of applicants with near perfect grades and GRE scores to pick from.
I'm not exactly sure what you should expect since very few people get B's in calculus and linear algebra, then an A in graduate real analysis. I would apply to a range of schools ranked between 20-50 and see if someone is willing to take a chance on you, since you clearly are capable of advanced math. It's not a good idea to apply to only UC schools, since their location makes them more desirable and harder to get into.
As for your GRE, it's probably not worth retaking.

I think the range of schools you're applying to is fine, although I don't think you'll get into the top 6 on your list.  Agreed on adding more 20-50, although you could go higher.  Your low GPA won't be a huge issue because you obviously turned it around after freshman year.  I wouldn't bother explaining.

Oh and Colorado State has a big ecology/spatial focus. 

You'll find censored data/high dimensional people at a ton of places - Minnesota has a big focus on HD machine learning (think Lasso). For software, UC Davis has a major R guy, Duncan something. For spatial, look at Ohio State (and lower down, Mizzou).  For functional data, FSU has a huge group of people working on shape analysis and a wavelet guy - one of their grads is also a prof at OSU now.  

Agreed with Bayes above. Usually 75/80% is the cutoff. If they ask for it after you apply (very unlikely), then tell them. It won't make much of a difference either way.

That's tough, I'm not sure there's a forum consensus on whether domestic students should submit GRE math scores around 70%  Most people lean towards only submitting 80+.  You're right on the border, so it probably won't help or hurt a ton.