I was also thinking about getting a masters before going to med. school would that Help? I can also go 5 years instead of 4 years for my undergrad would that be beneficial?
There are several things I can think of that I would do in your shoes.
If you get to the end of junior year and things are going better (Getting A's and B's consistently) and your MCAT is good, I'd go ahead and apply to med schools, making sure to include at least a smattering of DO schools. Previous to this, I'd have developed EC's as awesomely as possible, and studied hard for the MCAT so as to blow it away. If you don't get in anywhere with this plan, there are some post-bac programs that ONLY admit students who have tried to get into med school and failed, so I'd finish my degree, if the last year is spectacular I'd reapply, otherwise I'd do the post-bac route.
If things are not so awesome by the end of junior year (and I mean there is an upward trend but it's not dramatic enough) then I'd either take another year and possibly add a second major (more classes dilutes any previous GPA anomalies, another year gives an upward trend more time to prove itself, and the second major would look impressive on an app and show your interests are not narrow), or I would graduate on time in my chosen major and then do an MPH program. Once you have a grad degree they supposedly shine way less harsh a light on undergrad. Most med schools also like slightly older applicants.
You can also do something like get a non-science major in undergrad in something you really enjoy that comes naturally to you and take the bare minimum science pre-reqs while developing ECs. Then after you graduate, either do a post-bac program (one for people who haven't applied yet) or do it on your own: dedicate a year or two to studying for and taking the MCAT, working at a good job (either at a hospital or at a nonprofit of some kind would be good) and going to school part-time to take more upper-level science classes. Do it at your own pace, and if asked later about why you did part time classes you can launch into a spiel about your awesome job and how much you loved being a research assistant/crisis counselor/volunteer coordinator/whatever.
Basically, the name of the game is to balance perseverance with knowing how to pace yourself and not bite off more than you can chew. If your grades don't rock at first it may take you longer and it may take a bit of extra planning, but you can still come out as a competitive candidate with something unique to offer.