retake the pre-reqs if they are a C or lower for pharm schools. Math is a little tricky since most people only have 9 or so hours of it in college. Make sure you do well on the ones for pre-reqs and/or on the PCAT.
Most schools calculate Science and math together. Schools that don't appear to be the exception rather than the rule. Do well on the sciences and then try to take upper level math if it worries you but ONLY do it if you feel you can get a B or higher, A being most preferable of course.
Schools have a minimum GPA cut off. If you have that then there is nothing to stop you from applying. However, recent trends are useful for people who have lower grades to being with.
I had a year where I tried to withdraw due to family issues and have an F on Stats, precalc, and organic + lab. I can never get rid of that and many pharm schools don't do grade foregiveness.
However, I retook those classes and got an A in all of them except organic, which i got a B. I will then talk about it in personal statements later on to discuss what happened. Do the same and show a higher trend and this will barely be a blip on your radar.