Apologies for bumping an old thread, but I finally had an opportunity to watch the TWOK workprint myself today at UCLA. I'll be working on creating an updated version of my continuity script to go along with it, but here's some scattered thoughts:
The film is cut pretty differently in the first 45 minutes. It opens on the simulator, but then stays along with Kirk through the apartment, the inspection tour, and leaving drydock. Then it goes to Ceti Alpha V and Regula I.
The most interesting thing is to hear the difference in DeForest Kelley and Kirstie Alley's performances. So much of their dialogue was redubbed during ADR sessions.
Some lines are missing throughout that made it into the final and director's cuts - bits in the first Khan scene, Kirk and Bones after Preston's death, and so on.
The original Kirk and David fight scene was striking because David has the upper hand throughout. If not for Carol interceding, David would've killed his father.
Visual effects are unfinished throughout, although some of the initial shots of Reliant firing on Enterprise were actually completed. Didn't see a single VFX shot that wasn't used in the final cut.
The workprint ends after Spock leaves the bridge to get down to engineering while Enterprise is making its slow turn to escape from Reliant. Khan's kid on the transporter pad with the Genesis Device is not included (IIRC, they never actually got that shot completed). Essentially, pages 105 through 117 of the final shooting script are not included in the print.
Total workprint time was just under 1 hr 45 min.
Finally hearing all those clips is the next best thing to being able to go to UCLA to actually view the workprint (which probably won't happen for quite some time as it is). I just went through all of the audio clips and updated my continuity script of the workprint version, denoting all of the changes from the shooting script:
https://www.scribd.com/document/246301267/Star-Trek-II-Footage-Rundown-Workprint