I've read the shooting script. The only significant material that isn't on the DVD is:
1. McCoy's comeback to Kirk's 'drop in for dinner' line: "That's right, turn it all into a joke. Dammit Jim, are you that anxious to meet your Maker?"
2: A deleted line from Vixis when Klaa learns the Enterprise is going to Nimbus: "'There will be no peace as long as Kirk lives.' (quoting the Klingon Ambassador from the the last movie) Our Empire's highest bounty has been placed on his head."
3: As the Gailileo heads down to Nimbus, Kirk notices Spock looking disturbed. "You okay, Spock?" "I am fine, Captain. (on Kirk's look) Damn fine."
4: The aforementioned McCoy helping a redshirt scene. "Haven't seen a wound like that since med school - these people are savages." (hands the redshirt the 'bullet') "Here's a souvenir. Stay off that leg for at least two minutes."
5: The aforementioned Spock/McCoy lines near the end in the lounge before Kirk shows up:
McCoy - "Try this on for size. Has it occurred to you that the Great Barrier wasn't put there to keep us out...but to keep that thing in?"
Spock - "It has occurred to me."
McCoy - "Well? Doesn't that imply the existence of a higher power?"
Spock - "I will say this much, Doctor - we have yet to truly reach the final frontier."
That's it. That's all that's missing. Other than that, the missing Rockmen and the DVD deleted scenes, what Shatner and Loughery wrote is what's on the screen.
That's mostly correct--except there is a scene on the BOP before it attacks the Enterprise in orbit of Sha-ka-ree.
In fact the scene is shown on the 2-disc DVD during the interview with the two Klingon actors (with the dialogue muted.)
And just to be picky there are a few lines prior to Sybok showing McCoy's pain where Spock describes his 'power' as
"an ancient ritual, forbidden in modern times."
McCoy's line "You call this living...?" was followed by "...suspended between life and death by a bridge of pain."
Also, the fight scenes between Kirk's men and Sybok's forces were longer.
The scene between Kirk and 'Admiral Bob' had this exchange...
Kirk--"Klingons don't negotiate--they annihilate!"
Admiral--"That's why you have
to get there first!"
Sybok's takeover battle of Paradise city was originally much longer and the line, "My friends behold paradise!" from the DVD deleteds wasn't awful.
McCoy had a nice line about the 3 envoy's having "typical hostage mentality."
A brief extension when Spock has the 'rock-gun' on Sybok....
Spock, you can't stun me with that
weapon and I've always been
stronger than you. I'm afraid
you'll have to kill me.
They cut a few nice line to make room for some terrible stupid stuff.
So, what I'm saying is if you cut little tiny embarrassing gags that last a few seconds--there a few little things to replace them with that would even out the run-time a little bit and keep it from being a 90 minute quickie.
Link to script with above scenes/dialogue.