Ok, I am attempting to re-encode the video at 16:9 now. I tried to fix everything on the list that was not part of the original release.

FIXED! Typo in the DVD's disclaimer.

FIXED! 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.
FIXED! Beginning of the Kirk/Spock/McCoy reacquainted scene, the dialogue is slightly out of sync, then seems to correct itself.
FIXED! 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.
On ORIGINAL Audio glitch at 1:02:30 after Chekov says his line and prior to Decker's line.
On ORIGINAL Very, very subtle video stutter at 1:03:32.
On ORIGINAL Audio stutter at 1:04:36.
Missing Footage At 1:04:47, the word "medic" is heard, but no one is seen saying it.*
ON ORIGINAL! Audio stutter at 1:05:55
ON ORIGINAL! Audio stutter at 1:07:02.
ON ORIGINAL! Audio stutter at 1:13:12.
ON ORIGINAL! Audio stutter at 1:14:02.
Can't find this error Video stutter at 1:14:11.
ON ORIGINAL! Audio stutter at 1:15:08.
Can't find this error Audio stutter at 1:20:49.
Can't find this error Audio stutter at 1:33:34.
FIXED! 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.
ON ORIGINAL! Audio stutter at 1:42:09.
ON ORIGINAL! This might be just on the film, but the video has a black bar flicker on screen at 1:42:39.
ON ORIGINAL! Audio stutter at 1:55:16.
ON ORIGINAL! Audio echo from Ilia at 1:58:06.
ON ORIGINAL!Repeated audio at around 2:04:24.
ON ORIGINAL! Audio stutter at 2:07:21.
Can't find this error A frame skips at 2:14:47.

If you guys can find any more errors by tonight, I will include them in the changes.