The advice I've gotten from my previous PI's is that I should get into some of the lower tier schools that I've applied to, and possibly into one or two of the reach schools. Though my current position isn't in academic research, it's still research. My management goes as far as managing my team of scientists involved in developing and characterizing products, but is still a very hands-on wet lab type position. I've thought about master's programs, but I'm not sure I'd gain much, apart from a reboot to my GPA. I guess all I can do is wait and see...