Thanks for the input!
Excellent case made about the prologue. Very good point about it not being in the Trek idiom. It's out.
Last night, I dug out my old copies of the Marvel comic adaption and the Photostory tie-in book. They seem to be good models on how to break down the story to it's most important plot points. They trim a lot of the same elements I was thinking of doing myself. This is one of the movies that I wished they had done an audio-book of with one of the stars. It may have come in useful.