I have found than nothing sticks to POR once it is dry.  POR makes an etch primer in a spray can that will stick to POR tho.

The windshield guys that really know thier stuff will not apply urethane to fresh paint or paint of any kind.  ONLY primers/epoxys.

I think if i was you i would treat only the rusty areas with por,  then before the por has fully cured,  like about 2 hours later,  apply windshild primer.  It is called pinch-weld primer,  its black and bites into amost anything. 

This pinchweld primer is what all the glass installers swab onto the body before they lay down the urethane.  Any glass installer will have it.

Best part for you is that it is black,  so you can swab it all over your window chanel and not have to worry about the color!

sorry i was off line carl, as a former winshield tech , no urathane sticks to any type of wet paint very well or for long, i did lots of rust repare in the shop from bad winshield installs, i would us a epoxy primer then paint then urathane primer then urathane. you also have to prime the inside of the winshield to protect the urathane from the UV light.their is clear primer and black primer use the black

i used to fix them with the small touch up bottles but spray can cnd tire works well it just has to be dry same as the urathane primer