This article is from the rec.arts.sf.movies FAQ, by Evelyn C. Leeper firstname.lastname@example.org with numerous contributions by others.
According to Jerry Boyajian:
There are a couple of very minor bits, but the two significant (and
related) additions are:
--The details of the proposed operation to rescue Kirk and McCoy from
the Klingons, presented by Col. West (played by Rene Auberjenois) in the
President's office. In the theatrical release, this is completely
missing, though the easel with the plan diagrams on it seems to
mysteriously appear out of nowhere.
The second is a spoiler, so it is rot-13'ed:
--Gur eriryngvba gung gur Xyvatba nffnffva ng Xuvgbzre jnf npghnyyl
Jrfg va qvfthvfr.
Susan K. O'Fearna also suggests that in the arrest scene, they show Kirk
being cuffed, then show him being cuffed again be a part of the extra two