I wouldn’t worry about those Calc I & II grades. It would have been a much bigger problem if you aced those courses but performed subpar level on the more advanced ones (which you aced). You will need to retake the GRE and get at least a 165-167 that is no question. But before that we need more information:
(1) Tell us more about your MA classes (were they applied in nature? Were they close to econ phd classes? List books if applicable)
(2) What range of schools did your MA program place people in the past?
(3) Go to your letter writers with a list of schools (even including dream ones) and measure their reaction and see which ones they feel comfortable writing you a LOR for.