Apply to more schools (mainly because applying broadly never hurt anyone). But seriously I hope you take everything you read here with a grain of salt, because you have no reason to be even half as concerned about getting in as those here are making it seem. It's a crap shoot, and it's definitely not as simple as have a high GPA and things will work out. (PS my GPA was *much* lower than yours, and I didn't have any issues). My LORs included one of my PIs, and two professors; this is not abnormal.
