I just pulled my rear window to re-set it because it had slid down on the studs for the molding. I discovered there is a little rust, not to bad but enough I can really sand it of with sandpaper or a wire brush. Should i first paint it with some POR-15 and then go over it with pinchweld primer or should I just use the pinchweld primer? Any advice would be very appreciated I am hoping to re install it tonight or tomarrow.

You should clean it down to bare steel. Then primer with a good automotive epoxy and top coat. Pinchweld primer goes last.