First, we need to settle on a version. (Be warned; one of my infamous long posts ahead.)
* As Kad pointed out, before his death, Bernstein set the "final" version of the score in 1989. So let's use that as the jumping-off point since that reflects Bernstein's last wishes for the show. We've got that score, which reflects a particular plot line.
* With the score in place, we go back and shape the book around that, which isn't hard thanks to the narrative Bernstein and John Wells wrote to accompany the recording.
* There are two extant versions of the libretto available that can be licensed from MTI, the Hugh Wheeler version and the John Caird version (the latter of which draws on the other but also pulls from various sources including Lillian Hellman's abandoned original script and the Voltaire novella), and I'm sure the rest would be a mess of copyright problems involving the various estates, so we have to contend with what fits from either of those versions.
* Having a "set" score and a reconstructed book, one can then go about whatever vision they have in mind for the piece.
"There is no problem so big that it cannot be run away from."
~ Charles M. Schulz