A couple of comments here.. First I'll mimic what others have said about scores, it does not matter much as long as you get beyond the initial filter (usually 3.0ish). I had a lower GPA (3.2-3.3ish) than most of my cohort, but I had much more experience (3 years in academic research) which held a lot of weight through the application process. Once you get interviews don't be surprised to have to have to justify the lower GPA and just be honest when that comes up - they really don't care about your GPA otherwise you wouldn't get an interview.
Anyway, I went from a chemistry BS into a molecular bio phd (although the lab I settled into is much more biochem/chem bio than molecular), but I would be careful about picking places with only 1-2 PIs who you are truly interested in. I did that and (luckily) I ended up with the only PI in the department I was interested in, but it could have been quite bad for me. Not only will you have rotations to do in multiple labs, you have to take into consideration the department as a whole. Being the only lab in my department focusing on my field of interest makes collaborations more difficult and you can find yourself on an island at times.
The school I settled on was not the highest in the "rankings" (~50s), but I'm working with a PI who is well-known in the field I find interesting, so it worked out. However, if he was not accepting students or if I was not a good fit into the lab I would have likely had to leave the program because no other PIs were interesting to me.
