Well, having done only "The Corbomite Maneuver" shortly after getting the set, I can tell you - you'll need a LOT of free time. You really don't appreciate the amount of editing they had to do in order to stitch together scores out of existing cues. There is also a lot of repetition that you generally don't notice watching an episode. I was considering doing more, but that single episode pretty much spent my passion for it. Can you imagine doing "Balance of Terror?" Some cues are so sharply cut, they don't even make a good listening experience. Pop in the episode and watch when the Enterprise is firing on the Romulans, the same attack the Centurian is injured. The jarring cuts from "WNMHGB" are realy obvious on their own and a tough mudder to put together.
And, yeah, you'll need the VHS/Laserdisc prints at the very least to get close to an accurate account of the music.
However, if none of that discourages you, have at it and good luck! But you'll find that you won't be able to recreate every episode because of how some of the cues were edited together. Some cues were cross-faded to recreate how they originally sounded in their respective premiere episodes. Like "WNMHGB", "Amok Time", "The Cage," etc. At least the previous releases of those scores have many of the cues separate as originally recorded, but the cross-fading makes it tough to use the higher quality cues accurately. A library cue version of "One's Enough" from "The Doomsday Machine" was used in some episodes ("Mirror Mirror" for one) with a "sustain" at the end, fading out before the the triumphant exit music was supposed to come in. That other version is on the set, but it was attached to an alternate version of the exit music, so the sustain isn't there. So you can't recreate the final cues to "Mirror, Mirror" accurately. The drum hit in "Catspaw" as Jackon tumbles off the transporter pad was heard in some episodes on its own ("Obsession"). Also, that same cue ("Captain Kirk") was heard in other episodes without the drum hits, but doesn't exist on the set by itself. So, creating a fully accurate "isolated score" for "The Deadly Years," for example, isn't possible. Unless you can pull the music off one of the home video releases and wash out the dialog and sound effects.
I hope that isn't totally confusing.