I have made some side-by-side comparison between the US and Japanese LDs starting with the episode which has the most obvious audio changes, City on the Edge of Forever. I did encode both LDs with the exact same settings from my Pioneer player. Here’s a sample :
Picturewise, this is exactly the same transfer. Colors on the japanese release are a bit warmer, but this is the very same transfer. The exact same defects can be seen on both :
Surprisingly, the original “Goodnight Sweetheart” music has been kept on the Japanese LD, on both english and japanese tracks (even if the sleeve says the opposite).
There are some forced japanese subtitles here and there for scenes that haven’t been dubbed in Japan back in the 70s.
The Opening sequence looks like crap on the japanese LD and is from the second season. The original first season opening is on the bonus LD from the jap boxset.
The trailers are included AFTER each episode ending. Desilu/Paramount logos are not the same than on the US release. City on the edge have the Paramount zooming logo from 1968 whereas the US LD has the blue montain Paramount logo from the 70s.
The audio is of course much better on the japanese LD since its digital mono and can be transferred losslessly to a PC. The Japanese LDs also have chapters.
So yes, I would start from those japanese LDs, these are the only TOS release with the original digital mono sound.
Well, just from the scant details you included, the BR mono is the original. So the Japanese LD’s are not the only source.
Like I posted above, from what I can see from examining the audio streams, the original mono is preserved in the center channel of the 5.1 mix that first came out in 1999 in the 2 episode discs and then again in the clamshell box (which has Goodnight Sweetheart in City). The altered sounds are the mono sound, filtered and expanded to faux stereo, and added to the other channels in the mix to create a broader spacial feel to the sounds. They aren’t actually new sounds, but they are an alteration to the original, but the original is still there if you care to filter it out.