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None of your retakes replace your first grades. AMCAS counts every grade from every course you have ever taken. So in other words, AMCAS has no grade replacement. It’s hard to advise you without your MCAT. Have you been accepted to the RWJ program? When would you start(it’s getting late for a start this year).
 
my undergrad GPA will discount me from a certain tier of schools

Not sure why you still thinking "tier of med schools" with your GPAs and no MCAT. You should shoot for any med school (including DO). Sorry to tell you, 3.2 GPA in a social science at an Ivy is not impressive for med school admission.
 
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