One problem related to side/rear glass has been reported for the 1999 Ford F-250. The most recently reported issues are listed below.
The windshield on my 1999 f250 superduty leaks when it is raining. The problem has existed to a minor extent for several years, however, until recently the problem was not bad enough that I felt it needed repair. I first noticed the problem shortly after the warranty on the truck expired. Last week during a rain storm it was obvious that something needed to be done. I took the truck to a local glass repair shop, binswanger, in fort worth. The repair technician told me that this was a common problem with Ford f250's that he has seen many times and that it was more than just a leak. He said that the windshield was never secured properly from the factory and may come off the truck. The technician explained that the adhesive was bonded to the windshield and the paint but that the paint came loose from the metal around the windshield. So, it appears that I am simply fortunate that nothing catastrophic happened over the last 9 years while I have been driving the truck. I would like Ford to fix the problem.