Why were the original windows not standard?
The link Matt found (thanks Matt, I had forgotten about that) explains the thickness but it doesn't answer your question.
What we see as a "bar" through the original windows is actually a stringer and its removal speaks to the unprofessional nature of Earhart's entire operation. In January 1936, confronted with the need to deliver an Electra with a 50% greater maximum gross weight than the airplane was designed for, Lockheed eliminated all but two of the ten standard windows and left in place a stringer that, on the standard Model 10, would be cut to accommodate each window. As delivered in July 1936, the "10E Special" featured an immensely strong uninterrupted fuselage structure of stringers and bulkheads broken only by the cabin door. In January 1937, as the airplane was being prepared for the world flight, navigator Harry Manning (who had no experience in aerial celestial navigation) insisted on an elaborate "navigator's station" in the rear cabin. He wanted mounts for a pelorus (sighting device) at each cabin window, but the stringers would be in the way so they were cut out and standard windows installed. He felt he needed optically correct windows for taking star sightings so a special window was put in the cabin door and a large window was installed on the starboard side in the lavatory - all of which butchered the integrity of the fuselage structure created by Lockheed to accommodate the stresses caused by the heavy fuel load. The work appears to have been carried out at Mantz Air Service without benefit of Bureau of Air Commerce approval or inspection.
How is the book coming along?
The further I get into the story of c/n 1055 the more it becomes the story of Amelia and the people around her. The simple progression of first-they-did-this-then-they-did-that would be a useful guide in dating the many photos of the airplane, but it's the "why" the changes were made that sheds much-needed light on who she was and how her career and life came to a tragic end. The book needs to be broader in scope than I originally contemplated. The same thing happened with my first book. It started out to be a TIGHAR Tracks article, then a book, about the post-loss radio signals and morphed into Finding Amelia - The True Story of the Earhart Disappearance. I'll undoubtedly need the Forum's advice as I work out the boundaries of this book but, wherever we end up, everyone who has donated to the book project will get a signed copy when it's finished.