For the love of all things SciFi, please get rid of "Don't wait for the translator!". (And get rid of the translator guy). That's their most idiotic cold-war reference. Klingons have universal translators, just like everyone else.
Dried human blood is brown. Assuming that Klingon blood is, then that makes it far more believable that no-one noticed the dried blood on the transporter pad, until Checkov looked closely. Maybe you could make dried Klingon blood an unexpected dark color.
If you're going with the aspect ratio on the ST VI special edition, then you're going to have a problem matching Flashback footage to it. The first several years of new-Trek episodes have poor-quality video. Cropping & resizing will make it worse. They were mastered onto D2 - a low-end (lowest?) broadcast-quality tape, until the final two season's of Voyager. In fact, they are somewhat pillarboxed - black bars on the side. Also there's artifacting & other video problems that'll get worse with resizing.
ST-VI was Super35, and they opened the matte to close to 16:9, for the DVDs. If you trim them to 16:9, then you'll have less resizing to do with Flashback. (Phase-II-style edits would look ok in fullscreen, the opened matte means most of the camera work looks normal in P&S).
The biggest problem with Flashback is that Janeway is right there. She's obvious in almost every shot. (Makes Mulgrew look like a camera-hog, but the story is really about her being in Tuvok's past). Fortunatally, the scenes are replayed from a variety of camera angles. So it might be possible to find enough bits where it's possible to composite her out. When she's in normal uniform, you might be able to replace her head (far fetched), alter her hair, or use shots where she'd far enough to try to not-notice.
The nastiest bit is where Kang is on the viewscreen, and she walks right up and blocks the right side of viewscreen. I think that one can be repaired by compositing. But when it switches back to a view of the nebula, there's going to be a challenge. Thankfully, Takei's acting is passable in the sequence with Kang.
My Phase-II-style vapor-edit would only use a few of the Flashback scenes, and change the episode's story a bit. Sulu wouldn't disable the Klingons and head right back. Klingons have subspace communications, too. Sulu would cooperate until he was out of sensor range. Then he'd sneak back in. He'd save the nebula explosion trick, in case the Klingons caught him again (which they did).
Also, I'd, personally, remove all references to Dimitri dying. He was alive at the end of the original. (Or you could choose to composite him out of the viewscreen shot at the end). I consider his death to be another false memory - not as traumatic one as the virus's signature false-memory, but pretty bad. (Especially for a Vulcan who wasn't very cooperative with the emotion-repression as a child).
And then there's the small matter of Rand's rank being different in Flashback. That would require some very advanced compositing, maybe rendering, or you would have to choose her closer-shot scenes exclusively from one or the other.
The first event in Flashback, where Rand teases Tuvok about the tea, happens before the start of the movie. And Whitney (Rand) is suddenly a bad actress. (I blame it on the same Voyager directing that made Takei's performance Chacotay-wooden. Captain Sulu was awesome in ST VI, and suddenly awful for much of Flashback). Too bad, because there's actually a shot or two without Janeway.
Heh, no matter how many opinions any two Trek fans have in common, you will always find some thing(s) that they completely disagree about.
I'm sure it puts me in the minority, but almost all of the ST VI jokes make me wince. I remember the theater audience laughing where I was cringing. The ones that I hate require them to be out of character, in my opinion.
While the sabatoge discussion has humorous moments, it requires everyone but Valeris to be uncommonly dense. Then there's the jokes that make Checkov a comic-relief character. Checkov's character had lame dialog in ST II, then he became more & more of a dufus. He bounced back to normal in Generations. (In TOS, he had the "Russian invention" thing, but it eventually became clear that he was joking with them). And my gawd, the translation scene. Ick.
The only thing that earns unreserved laughter, from me, is the whole "I'm going to kill you anyway, so I might as well tell you." sequence. And I know few people who share that opinion. If my version ever gets realized, it will be fairly humorless.
One more thing: Normally, a PAL DVD would give you more vertical resolution (if it were scanned, to PAL, from film). But they did an pitiful job of resizing the NTSC sources to PAL. Modern software would do a lot better. So if you can get ahold of the NTSC version...
Another more thing: That bit with Uhura struggling with books to do the translating. Yeesh. Even if they could pick up on the universal translator's generated voice (I doubt it, that's more believeable for computerized voice impersonation), I don't think their equipment would pick up on normal Klingon sentances. She should be reading from a monitor. Unfortunatally, I think the scene would have to be cut. Or have the two bored Klingons challenge them for ID, then switch away to the Excelsior, or switch to Kirk & McCoy. The audience can just worry about it until we see the Enterprise crew again. Might also be able to crop the books out and have Uhura start to say "We are the..." and then switch.
Edit, again: Vertical resolution, not horizontal.