I saw only a handful of marks on the print. Because they were limited to single shots, I think they're baked into the opticals. I don't know how accurate it was to the original release, but the contrast and color timing looked right to me.
All the dirt I noticed matched the blu-ray (as one would expect, since it's the same transfer). The worst is was on the shot of the bottom of the saucer leaving drydock. Must've happened while they were originally editing the film, since it's not in the (longer version of the) shot in TWOK.
Agreed on the big screen really helping the scale of the movie (though my theater didn't zoom in the projector to cut off the letterboxing, so it a bit shrunken within the screen). I'd never heard any version of the film in surround before. There was a lot more going on in the mix that I'd ever noticed before in the cargo bay and engineering scenes. A lot of added echo in the dialog, and a bunch of nearly-intelligible background chatter that's mixed down to nearly nothing in stereo. And this movie is
loud, and I love it. The jump-to-warp scenes melted my face off, and the old fire-alarm red alert klaxon was wonderfully ear-shattering. When I get back to my HD mostly-recreation of the DE, I'm going to have to be careful with the sound mix, to make sure I can preserve all that on the off-chance I'd be able to view it in a fancy home theater with good speakers.
Aside from the old red alert, I, too, regretted that it was the theatrical cut, a little. I think this is the first time I've ever watched that version all the way through, growing up on the SLV on VHS, then switching to the DE (sigh) almost two decade ago. A lot of scenes are sliced down into incoherence in the theatrical cut, and nearly every instance of the crew figuring something out or working a problem is eliminated, so it looks like they've just suddenly gone psychic or peaked at the next page of the script, never mind all the character beats the movie can't afford to lose (the transition to McCoy beaming up is like the opposite of a
"Gilligan Cut" joke; "I'll see to it he beams up" -> McCoy beaming up). I really wish they'd made a new version of the SLV for blu-ray, even if they didn't have the interest in recreating the DE in HD.