After a lot of thought, debate, and planning (and a little luck), I've been able to put the foyer window back to it's original design. By a stroke of luck and coincidence the seller of the garage door I bought on EBAY was also a master woodworker down in Cape May and offered to remake the pair of windows from a picture I obtained from the Hall family.
They are stain grade pine as original, with salvaged old (wavy) glass used. Originally these were casement style and would have been hinged on the side, but I opted to seal them in permanently which will be a bit more efficient, and I already have plenty of ventilation.
Once nailed and caulked from the outside I turned my attention to the inside replacing the old sills. After a little tweaking they fit like a glove. Then replaced jamb pieces temporarily (they still need stripping) and finally some of few remaining original casing. The final result looks better than I could have hoped and definitely ties the foyer together much better than those aluminum double hung windows ever could.
closeup of new sill and windows
The windows were hand made by John Hassay of Cape Island Woodwork, just outside of Cape May, NJ. He is restoring an old Quaker meetinghouse dating back to the late 1700's. He just finished working on this year's 2007 Cape May Designer Showhouse and has been involved with several other high profile restorations including Congress Hall in Cape May a few years back. I highly recommend him. I decided to have him make the 3rd floor dormer windows as well which have the same design as the main staircase landing window. One window survived being used to fill a busted sash in the garage, so at least this time he has an example to copy from.
windows with trim reinstalled