Hi Banksy,
I'm at a similar point to you- I am working in a biomedical lab while applying to PhD programs (in public health, though, I'm changing fields). A few comments:
It sounds like you have some really good connections at the schools you want to go to, and I think if you use that to your advantage, it could make up for the numbers. If you have people on the faculty who want you in their lab, and know you do good work, they will fight to get you in. I don't think there's any reason not to rely on that- I have good numbers, and I am freaking out cold-contacting faculty, because no numbers make up for having someone willing to take you on as an advisee. The way I see it is, you have landed a really good job, and from the sounds of it you have really proven yourself since being there. The publication process takes a really long time, but having a supervisor who is able to enthusiastically recommend you to his colleagues is for now the best concrete demonstration you have of your accomplishments. If you can get the senior scientist to introduce you to some of his connections, and start a dialogue, you probably have a really good chance.
As far as the GRE goes, I think in biological sciences the verbal might count almost as much as the quantitative section, although it might depend on the field you are in. If you do end up retaking it, I highly recommend this website: http://www.brainscape.org/ It is a flashcard program for GRE vocabulary, and although I generally don't like flashcards, this was an absolute lifesaver for me. I don't know what I would have gotten before using it (probably not a good score), but I ended up with a 700 on the verbal.
Overall, it sounds like you have what counts most in your application, which is demonstrated dedication and ability in research. Your work at your current job will probably be a real strength for your application, so definitely take full advantage of that.
Good luck!
Kim
