The cue sheets, according to several individuals involved in working on the boxed set, are Paramount's internal property and not able to be released. Jeff Bond did say, however, that he included several in his The Music Of Star Trek book by typing up the information himself.
Of course he immediately followed up that information
by saying something along the lines of "if any of you want to volunteer"... ha ha, very funny Jeff, you going to check them out of the Paramount library for us?
So, aside from the small handful in the book (which I could dig up, if anybody's interested), it's all up to listening. The other problem is that there were cues that were created from cutting up and editing together several different cues that are only presented in their original format on the box. Putting complete scores together is therefore a little bit more complicated than just making 80 playlists, unfortunately.