One thing I would plan on is pulling the rear window out. You probably have problems in the channel that the gasket sits in. You will want to replace the gasket too.

I have no experience with POR 15, so I can't offer advice.

Any time you treat a surface with a rust product, I would then sand it off just before any plastic work. You want the metal treatment to do it's job, which is to chemically change the "iron oxide" (rust) into "iron phosphate" (which is just a dead gray material) but body filler will not stick to the metal preps I've used, so you'll need to sand most of it back off after treatment.