1. Kirk actually trying on the glasses in his appt.
This is what I wrote down during the scene:
MCCOY
No, no. No, you pull them down on your nose. That’s it, now you look at me over the top, and you read the printed matter through the bottom.
KIRK
Oahhh...
(this is a terrible line reading)
2. Terrell seeing the baby inside the cargo carrier/home
Yes! In fact, the scene is so centered around the baby (who doesn't appear in any other scenes in the version I saw--though it was missing the ending, where the baby has been glimpsed in certain production stills) that I found myself having quite a bit more respect for the editor of the movie.
TERRELL
You know these look like cargo carriers.
CHEKOV looks in the window, sees the CHILD. CHEKOV screams.
CHEKOV
A face! It was like a child.
TERRELL
You’re crazy.
CHEKOV
I saw it.
TERRELL
Hey, this looks like an airlock. Give me a hand.
--
TERRELL
...crash-landed, then where’s the rest of the ship?
TERELL walks into the next room, sees CHEKOV with the CHILD.
CHEKOV
I told you. I told you, I saw a child.
TERRELL
(to child)
Hey. Hey. Now look at that. What are you doing here? Where’s your mommy and daddy?
This is when Chekov realizes this is the Botany Bay.
TERRELL
But what about the child?
CHEKOV
Never mind that! Hurry! Hurry!
TERRELL
Chekov! What’s the matter with you? Chekov. Chekov!
CHEKOV
C’mon!
TERRELL
Well, what is it?
CHEKOV
Hurry!
3. The Sulu promotion scene (I really doubt this was in the rough cut)
Here's how the scene plays out in the rough cut I saw. Takei has long accused Shatner of ruining the take, and in my eyes, that's exactly what happens.
SULU
Well, I’m delighted. Any chance to go aboard the Enterprise, however briefly. It’s always an excuse for nostalgia.
KIRK
Well, with Spock as Captain you don’t think I’m going to turn anything up, do you?
CUT-AWAY to STOCK from TMP
KIRK
(looks down at Sulu, looks back up)
By the end of the month, you’ll have your own command, the U.S.S. Excelsior.
MCCOY
Well, congratulations, Commander.
SULU
Thank you, sir. I’ve been looking forward to that for a long time.
KIRK
Well I for one am glad to have you at the helm for three weeks. I don’t think these kids can steer.
4. After Kirk & co. view the genesis tape & is notified Reliant is near---Kirk mentioning Chekov is aboard Reliant
There's just a throw-away line:
SPOCK
Reliant? Here?
KIRK
Chekov is on Reliant, isn’t he?
5. Khan calling himself by full name 'Khan Noonian Singh' and calling himself a caged eagle.
Didn't take a note of anything like this.
Hope you won't think I'm nagging for too much info--it's just I've been fascinated by TWOK's script/cuts since seeing the 'TV version' in 1985 and owning the script since 1989. It seems the movie would have run about 7 or so minutes longer with the additions you saw.
The version I saw was 95 minutes according to the catalog entry, though since it was missing the ending I'm not sure how that works out. Honestly, despite my enjoyment in getting to see these scenes, I almost universally agree with their deletion from the finished film.
The last alternate line of dialogue I wrote down was from Kirk. In the film, I believe he says "Z-minus 10,000 meters." In the rough cut, the slightly different:
KIRK
Descend 10,000 meters.
The rough cut ending not long after that, although I didn't indicate precisely when in my notes.