I have a very small update to this that I’m putting out. I rendered V3 out awhile back to correct some small errors, particularly a jump cut that I accidentally introduced. I was waiting and see if there were any bigger changes I wanted to make to justify a new release, but since there aren’t, I might as well release this now.

V3 changes:

added Grace Lee Whitney (as Janice Rand) to the list of co-stars in the opening credits. She was treated terribly during her time on the show, and I think her name deserves to be next to the rest of the original cast (some promotional materials featured her similarly).
fixed issue with the BD footage, where aggressive DNR caused the bottom left part of the frame to smear and warp. 12:12
fixed issue in the original DC effects where the shuttle disappeared for a frame. 13:00
fixed one frame editing error I introduced 15:21
The original effects have an issue where the shuttle moves, but the background is frozen. They trimmed the beginning in the DC, but when matching the edit, I trimmed the end of the shot rather then the beginning, as I didn’t know why it was shorter. Now matches the DC. 20:38
fixed two frames of encoding garbage from the HDTV 26:37
The audio is now the untouched dolby digital track from the DVD (not rencoded) until the end credits, when it seamlessly cuts to the new end credits music. This saves some space and preserves Blu-ray compatibility if you want to remux.

Anyone who PM’d me previously should have the updated version in their inbox, as I have updated the links.