How do I get rid of this rust in the trunk?

Here is my $0.02. First of all, IMHO, don't bad mouth POR15. Had it not been applied, you would most likely be replacing the entire, swiss cheese rusty trunk. The POR15 probably stopped the rust dead in its tracks. I didn't get a feel for what your plans and desires were, since it was not mentioned in the original post. You said the metal was good except for the pits, so that means that some form of repair could be done. I don't know how strongly you want to replace it to make it perfect. Personally, I would cut out the whole trunk and replace it. Not bragging, but that would probably take me about the same amount of time as fixing what is there now. Besides, I love to cut and weld. If you can't do that of just don't want to, I would do something similar to what MoparMike1974 did (Which looked AMAZING) without the blasting. Use stiff wire brushes, wire wheels, or whatever, to knock off as much loose rust as possible. Then use SOME type of rust converter. I have used one that is Phosphoric Acid based. DO NOT SLOP IT ON HEAVILY. After it does its thing and turns the rust black, wipe it off with damp rags with warm water. The put a few teaspoons of baking powder in about a quart of war water and wipe it down again (damp rag, not gushing). Let it dry thoroughly. Then you are going to prime the entire trunk. I would use epoxy primer. First, scuff the entire area (treated area and entire trunk with 320 dry sandpaper. Then blow the area out, mask accordingly, use wax and grease remover, and spray the epoxy primer. After waiting the amount of time suggested on the paint can label, scuff the areas that are pitted with 320 grit and apply a skim of body filler. Sand and repeat until pits are gone. Regular filler will work fine. Then scuff the entire area again, prep and mask, and spray with whatever primer you like. Then it will look perfect and be ready for paint. Easy Peasy Lemon Squeezy.BTW, while in the USAF, I was stationed at Mather AFB twice; once as a Nav student, and once as a Nav instructor. We loved Sacramento.

Awesome, thanks for the step by step guide. I'll be following this when I'm out there this weekend!

Thanks for saying kind things about Sacramento, don't hear that very often from anyone not currently living in Sacramento :D