Jim, My AD started life as a 3 window. I had a light bulb moment to do a roof swap and make it a 5 window. That seam is where I split my cab(s) and did the surgery. There are a lot of spot welds holding the top of the cab, the roof, to that lower back panel and yes, there was a lot of rust on those pitch welds between the body half’s. I cleaned up all the rust at that location and then primed everything, and then used a generous bead of seam sealer between the two halves before I welded and screwed the pieces back together. As there is no movement between those body parts I think that if you clean up that area real well and prime it, and then use a quality seam sealer before paint, it should make for a clean and long lasting repair and future rust or cracking of the seam sealer shouldn’t be an issue. Mine is
Still Solid 30+ years later.
Good luck, Dave