Ziz said:
Maybe you could also re-master it in anamorphic, since others have suggested the fixes for it.

That is the plan, but I am going to need help with the settings in Adobe Premiere for 16:9 from a 4:3 AVI

This list was made by "eldiablosuizo". I want to thank him for making these notes. Just to let you all know, I don't plan to fix any of the audio problems that are part of the original sound mix. If the error was on the original, it's going to be on my preservation too.

Don't know if this could be fixed, but when Kirk and Scotty see the Enterprise for the first time, there is a reflection in the window. According to my memory, this was not in the Special Longer Version, added to the Director's Edition to add more resonance to the event (but I was personally bugger by because the reflective properties were not retained throughout). Again, you might not be able to fix this and, in the grand scheme of things, doesn't detract from the flow, but, since this is what seems like a purist effort, just F.Y.I.
Beginning of the Kirk/Spock/McCoy reacquainted scene, the dialogue is slightly out of sync, then seems to correct itself.
After McCoy says to Spock, "We just happen to be heading your way" (57:58), there is a lapse of footage for a split second, followed by Kirk's line.
Audio glitch at 1:02:30 after Chekov says his line and prior to Decker's line.
Very, very subtle video stutter at 1:03:32.
Audio stutter at 1:04:36.
At 1:04:47, the word "medic" is heard, but no one is seen saying it.*
Audio stutter at 1:05:55
Audio stutter at 1:07:02.
Audio stutter at 1:13:12.
Audio stutter at 1:14:02.
Video stutter at 1:14:11.
Audio stutter at 1:15:08.
Audio stutter at 1:20:49.
Audio stutter at 1:33:34.
Another Director's Edition shot at 1:36:53 with V'Ger in the background where once was a black background. Again, just for purist's sake.
Audio stutter at 1:42:09.
This might be just on the film, but the video has a black bar flicker on screen at 1:42:39.
Audio stutter at 1:55:16.
Audio echo from Ilia at 1:58:06.
Repeated audio at around 2:04:24.
Audio stutter at 2:07:21.
A frame skips at 2:14:47.

* This is the edits big snag. This is the section where we run into missing footage. For some reason, there is missing footage foe parts of this scene. The few missing sections have not made been release in letterbox anyplace. As far as I can see, there is no way to fix this error without the scene becoming more noticeable then it is now.