I'm interested in clinical research for pharmaceutical companies, not really sure what path I should take. I did not take Orgo II and got a D in Orgo I so I am afraid I won't get into MS programs when I apply.
You need to look at the requirements for each program that you are interested in. Some will and some won't require Orgo. If they aren't really clear, e-mail them to ask before you apply. I would look at the coursework carefully too. You'll want something where you can choose your courses to suit your goals. There isn't a need for you, for example, to take anatomy.
Admissions wise, the ad coms will want to see that a) you are academically talented enough to be competitive and b) that you've thought through what you need and chosen their program because it is a clear match for you. If you can prove those two things, you have a shot.