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.
Putting complete scores together is therefore a little bit more complicated than just making 80 playlists, unfortunately.
It seems odd. Paramount will license/authorize/sell all types of ST material and media, but not the eps cue sheets? Not even transposed into a simple playlist?
Which leads me to say... yes, I suppose I am just looking for 80 playlists based on the TOS box set. Each eps complete score probably is more complicated as you suggest. But I'd be satisfied with simple playlists and eps track listings. I'll work on it.