Hey SquigglyFace!
Congratulations on your recent industry success! There is certainly going to be a way to incorporate and frame those accomplishments into your application such that they are beneficial for you. The extent to which your industry experience will ameliorate the less impressive aspects of your application will depend on how you construct your "story" so to speak. You will want to discuss (so long as this is genuine and accurate) how your academic adolescence, lack of study skills etc. gave way to a re-invigorated research superstar, whose accolades are now evident in your productive career and steep professional trajectory. A way to demonstrate that you graduated with those high-level study skills would have been to enroll in, and ace, some grad classes at a nearby research university, but that is not essential here.
I might caution you to not put all of your eggs into the industry basket when it comes to LORs. You mention the director, CEO, and CMO, and it is good that they have strong connections. But for PhD applications the most important connections will be among faculty members. The CEO (is it de la Zerda?) or CMO may be quite valuable, especially if he/she is a faculty member in biology (and not just the medical school), and especially for applications to Northern California schools where his name might carry even more weight, and especially if he can comment about specific contributions that he has seen you make (a specific, detailed LOR from a director will generally carry more weight than a generic one from an executive). The more personal those letters are the better.
It might be a good idea to use no more than two letters from your current employer. And I hope that others will comment on this also. But if your three letters are all coming from a single industry entity, that may not give the admission committee the breadth of opinion on you for them to believe that they have a good feel for how your work has been received by PIs. And if all 3 LORs came from the same company, the details might be somewhat repetitive. Does that make sense? If you have worked in two academic labs and one industry lab, I would use a letter from each. Especially the professor in whose lab you completed your honors thesis... that could be a very strong letter. Caveat: Do not use a LOR from any lab you have worked in where you don't believe the letter will be at least good. (And three excellent LORs is better than 3 excellent + 1 fair LOR.)
Other things to consider: which research/work experience most closely reflects what you want to do your PhD research on? And did your undergrad PIs have reputation/connections of their own that can be helpful?
You probably don't want to hear this, but I would also consider re-taking the GRE. It's not lethal for you, but it takes a lot to overcome a low GPA coupled with a mediocre GRE. Getting your scores into the 160s, just 5 total points of increase, would improve the optics of your stats enough to erase this from being an issue. If there is a local, short-term GRE crash course you could take, I would give it some thought. It's one variable you still have a good amount of control over.
I'm not the best person to tell you where to apply, but I wouldn't try for the ultra-competitive landing spots like Harvard/MIT/Rockefeller unless you feel you have a specific "in" at one of those schools. If you feel you can reach for Stanford because of your industry connection, go for it, but yours is a slightly non-traditional path, so apply broadly, and apply enthusiastically. Stay aggressive. I wish you all of the best in your research future!
