I just purchased a 1949 Ford Convertible. The side rails are sagging in the middle which will not allow the windows to be fully closed.
Does anyone know how to fix this problem?
I don't fully understand what you mean by "side rails", but the first thing I would do is get the car up and crawl under and check out the body mounts. If you are referring to the top, please ignore this suggestion.
Ford and Mercury made manuals showing all the parts for the convertible top, it's adjustment and alignment. If you look carefully at the various parts of the top mechanism you will find there are very small allen head adjustment screws for the rails as well as the places the top mechanism is secured to the inner body panels at the rear bottom of the top. Adjustment is a very tedious process as the parts may have worn badly over the years. The top castings are die cast zinc and not very strong so be careful.
I think this is the book. It has a section devoted to convertible tops. https://www.scribd.com/doc/249258710/1949-1950-1951-Ford-Passenger-Car-Shop-ManualAlso, there may be another person who has restored a 49-51 ford convertible that can help.