I would use the overall GPA your undergrad transcript shows when applying, and unfortunately mine does do + and - (which sucks since 1/2 of my grades are A-). To calculate your major GPA use
http://www.iastate.edu/~registrar/gpa-calc/gpaCalculator.html
I've heard most med schools will average the grades if you retake a class, so if you get a C then retake for an A they count it as a B. Thats why I didn't bother retaking the C+ I got in calculus.
Overall it's not a big deal, the motto is no longer 4.0 or you're f'ed.