Reviving this semi-old thread. I'm repairing parts of the the body on my year round use LJ and am painting the whole vehicle. Here are a few things I've done to avoid future rust problems. There have been and will be more.
Front fender rust was mentioned above. The problem is the support panel that is located under the flat top of the fender. I bought replacement fenders and I could tell that they were barely painted between the two sheets of metal. The original stock fenders were better but they eventually rust out too. There is no way that you can apply rust protection in this area. I question how much support the panel provides so I just cut them out. I've since painted the fenders and I don't anticipate any problems.
I also replaced the windshield and frame. I was able to inject Fluid Film in the top of the frame and down the sides from the interior. The holes for the top frame and hard top clips is a good spot. There is no way to get to the inside of the bottom of the frame though. This is really the only part of the frame that is a rust spot and it's bad. A little unusual but I drilled two 3/8" holes through the frame just behind the windshield wipers. They're visible but partly hidden by the wiper arms. They don't jump out at you and with a dark Jeep they would barely be seen at all.
Always curious to see what others are doing!
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Fluid Film 360° Extension Wand for spray cans by Fluid Film: Amazon.ca: Home & Kitchen