Alright, it might be too late for this, but I just had a thought and felt I should suggest it, just in case. Hell, maybe this is how you did it to begin with.
Anyway, I recently downloaded, through Pirate Bay, a very nice-looking 720p Blu-Ray rip of TMP. I started watching it, but stopped for several reasons - one, all subtitles, including Klingon and Vulcan, are included in the English subtitle channel, requiring it to be turned on and off as needed, which irritates me; second, the primary audio track is Russian stereo, though the secondary is English 5.1 (it's just slightly annoying); and third, I'm encoding video and downloading torrents all at once, so VLC started stuttering hard not 10 minutes into the movie.
So I decided to pop in my Director's Edition DVD instead, which I assume you used as a starting point for this project.
My God what an awful transfer.
Now, since there's been a lot of Director's Edition effects that were noted as accidentally being left in Version 1 of your preservation, FF, and the DE transfer is terrible to begin with. My suggestion is, basically (don't shoot me, please!) - start over, using the very good Blu-Ray transfer as the backbone (this would, unfortunately, require subtitles to be added manually), and adding in the additional shots as needed. This would make the transfer much better throughout, and would eliminate (hopefully) all of the Director's Edition effects, including ones that may have been missed. It also uses the original, no-star-background credits, and the blank-screen overture instead of the Director's Edition credits.
There's a controversy over DNR being applied to the Blu-Ray release, but it isn't noticeable at all upon conversion to standard def (since most Blu-Ray DNR controversies stem from the studios using the exact same DNR levels they did for DVD, it's just that the higher resolution makes it noticeable).
I honestly don't expect you to do this, since it would require starting over from scratch, but I think the overall benefits outweigh the hassle. Then again, you've already gone through so much hassle with this project that I wouldn't blame you in the slightest if your response was "Fuck off, I'm not doing that." Just a thought I had, and I would have regretted not bringing it up.
--edit--
As a side-note, I'm strongly considering using this as a base to create a Theatrical Cut DVD preservation, since many don't have Blu-Ray players or the capability to watch HD MKV files on their computers. I think a 3-disc set with that, the Director's Edition, and your Special Longer Edition preservation would be absolutely perfect! Does anyone know if the theatrical mono/stereo mix for the film is available anywhere (I assume the Blu-Ray's 5.1 mix is new)?