First, 40-90 minutes in PFA only fixes the peripheral tissue. The center is still raw. A mouse brain needs several days to completely fix. If you are using frozen sections, antigen retrieval is a needless step. Are you doing a fixation step on the slides after they are cut. Methanol, acetone, PFA, etc. If not you are killing the antigens with the first few steps of your procedure.
Please post your staining protocol.