OH, second thought. Use four or more nuts nearly all the way off the stud when loosening the window. Ford's sealant remains pliable forever, but some of the other window sealants available dry semi-hard and are suceptible to leak over time. If that window was ever replaced after the factory it is very likely that a different (cheaper) sealant was used. Over time, vibration loosened the seal, and you now have a slight leak that will only drip when water has sat on the leak area for some time. That's why you can't find it by soaking it with a hose. Use a lawn sprinkler and let it sit for an hour or so- you'll find your leak then if I'm right.
If that sealant was used, it will require MORE pressure to loosen, and could very likely pop off at once which might break the studs if you have only 2 nuts holding the window. It will also be more difficult to remove from the body of the car. You might need a razor paint scraper- just be careful not to scrape paint where it will be visible. I had one window like that on the Aerostar. Scrape off as much as you can- you probably won't be able to get all of it off. Chemicals that can remove the sealant, remove paint. You might want to get some primer or Rustoleum paint to cover deep scrapes- although excess sealant should do the trick.
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