The top jambs had "ears" - extensions that allowed the window frame to be mortared securely in place.
Where the stone got in the way, the original carpenters cut off the ears and inserted wood pegs for keying the bucks to the masonry.
The replacement sills matched the profile of the originals; they came primed and cut to length, but the carpenters had to scribe and cut out the returns on site.
The author's crew used a two-part epoxy from Hilti that is installed with a proprietary gun. The long nozzle on the Hilti gun was helpful for injecting the epoxy through the thick window bucks.
The author's crew also used a single-part epoxy from Sika that is delivered with a standard sausage gun.
To attach a new wood window frame to the stone with threaded rod, the author first drilled a hole large enough to accommodate the washer and nut, using a wood countersink.
To avoid ruining the bit, the author continued drilling through the wood with a 1/2-inch masonry bit until he hit the stone. Then, with the frame out of the way, he continued drilling with a 5/8-inch masonry bit, making a hole large enough for the 1/2-inch rod and the epoxy.