It's a 1965 Buick Skylark and yes the top was restored and it has been all lined up with the windows and rubbers (PITA!).
What you are saying all makes sense, thanks. On the "fillers" some rubber washers sound like a deal.
On the measurement being after the bow height has been set doesn't make any sense to me. The only think you could change with that measurement IS the rear bow height, or am I missing something? How do you "set" the rear bow height? If you held it there some how (being it falls freely) at a certain height, setting that 17 5/8" distance would require you to change that bows height, would it not?