Ok, I can't remember since I have only seen the extended version, so it all blends together. The larger point being that the blood of the assassin is different from the Klingon blood earlier, so it is used as part of the reveal.
The Scooby-Doo ending was included in the home video version for years. On the blu-ray release, it is (thankfully) gone.
Were there two versions of the movie distributed to theaters?Well, Romulan ships in TNG are green...
The Colonel West version of TUC is a rather visible part of the Trek canon in having seen wide distribution in movie theaters - it's not as if it could be classified as a "cut scene" in the traditional sense.
The only other bit of Trek where anything even remotely similar happens is The Motion Picture, with its various versions, but those explicitly contradict each other (the V'Ger cloud can't be 2 AU and 82 AU wide simultaneously, you have to pick one size over the other).
I thought it wasn't changed to 2 AU until the TMP-DE, which was supposed to be the definitive and canonical version of the movie
Kor