Having seen all but Caroline or Change (although I have seen select performances from the show), I would swap out Fly Fly Away with What I Did For Love.
"Sit Down You're Rockin' The Boat" from GUYS AND DOLLS. One of the best 11 o'clock numbers ever. If that song doesn't fit the mold of 'a song to wake the audience up near the end of the show and send them out smiling and singing' I don't know what does. The '92 revival was thrilling.
I think "Is Anybody There?" works so well because the moment really begins with "Compliments", and the arrival of Abigail's shipment of saltpetre (Adams high), Washington's most recent and most doleful dispatch (Adams low), and then the song itself (Adams resolute). A real roller-coaster ride, and terrific theatre writing.