In Philly, the old WKBS-TV Channel 48 reran STAR TREK as complete and unedited for a time in the early 70s - for at least one complete run through the 79 episodes.
While I don't recall seeing the NBC snake logo at the end, I DO recall at least one or two instances of the NBC peacock still attached at the front. And I don't think they ran the next episode trailers.
Also my memory of the trailers is that the first season ones were different than what we see now. The "STAR TREK - NEXT VOYAGES" screen didn't happen until the second season. If memory serves, first season STAR TREK used a more traditional network promo with a voiceover saying "Next week on STAR TREK..." as some scenes played out.
When they first started either showing the trailers in TV syndication or on home video releases, they rejiggered the first season promos by appending the "Next Voyage" screen.
As for the assembling of the cue sheets, I think a lot of us with the CD box set would like ANY kind of useful cueing options for the episodes. If it's been slightly reworked - that's a minor consequence in the scheme of things. Just knowing that there's a formula out there for reconstructing any episode's score would be a plus. Whether it was night-of-first-broadcast or not is not of primary concern to most. Most people weren't around when NBC first aired the show (I WAS!), and no-one has accurate enough memories to know for sure which cue goes where.
What we have these days on the mono Blu-rays, or the DVDs will have to suffice for the re-compilation of such cueing sheets. So get busy guys - while us old geezers are still around to benefit!