If we're worried about a confusing ending, how much more confusing will adding the Borg make it? How can we make it clear that V'ger helped create the Borg? I like the idea for maybe a post-credits sequence (looks like we're going to have a lot of pre/post credits stuff in this edit!).

Idea: add some kind of morse-code-like sound to the "V'ger Disappears" sequence, fading out as the E appears. Then, after the credits, have that sound fade in as the music fades, then show a cube under construction or alone in space. Signal stops suddenly, maybe have the picture cut at the same time.

If the sound is subtle enough in the main film, it might work!