I really don't know how that would fit..I'd be open to suggestion but I would suggest sticking to Goldsmith stuff.

re: the Prologue - what about just keeping the existing prologue music? Other than that I agree that it should probably be something associated with the show, It should be an impressive reveal when the movie theme begins.

it felt weird getting this new theme and then changing it again with ST2, only for it to re-emerge later.

Well, it WAS the Motion Picture theme that later got reprised elsewhere, just like the title fonts, not so much a definitive "this is what star trek is now" theme.

That said i've been tinkering with rebuilding a version of the intro and Klingon theme from TMP using more recent cues [mostly from star treks 5 and 8] - I'm attempting to keep it as close as possible to the TMP version.