OP: AMCAS/AACOMAS will look at all GPA. There are tons of special cases in applications. Some applicants go to schools where there are no grades!
It will all come down to classification as to how the application services will break up and look at your GPA for UG vs. Grad GPA. I would contact AMCAS and AACOMAS (if you're applying to both MD and DO schools) and ask them how you should categorize your coursework on the application.
As far as which classes you may need to retake: Get an MSAR (Med School Admissions Requirements) and look at the profiles of all the schools you're interested in applying to. They have their basic requirements there.
Most schools of course want the following courses with lab components:
2 semesters BIO
2 semesters Inorganic (Gen) Chem
2 semesters Organic Chem
2 semesters Physics
Some also want Calculus, Biochem, among others so you'll need to make sure you meet their requirements.
Of course you'll also need the MCAT, which differs from the PCAT (if you've taken it) because it offers physics and harder organic chemistry (based on what this year's pharm-D applicants told me).
Completing all of this appropriately I see no reason why you would be turned down, even with a Pharm-D. You'll need to show compelling reason why you want to switch careers,
and probably need to work as a pharmacist to back that up.
I don't think a PharmD will hurt you if you have appropriate reasons to switch to medince.