It would also be possible (and possibly much easier) to make the triangular stock glass functional. In the '50s and '60s they were called 'wind-wings'- and were for effective cabin ventilation since A/C was not common in those days although available.
Using far cheaper plastic for custom full length side windows as prototypes would be my suggestion.They could easily be made and tinted, too. They would eventually be scratched by the usual 'whiskers' used in side windows, but should last a year or two- long enough to see if its worth it to you for the high cost of custom glass side windows.
For both jobs, I would enlist a really good hotrod car builder. This is not quite the typical home-shop project.