To answer your question though, the cut I was talking about was from the ship shot to the lab. Logically the way the movie is now it feels like it should be the Logos returning for the reasons you mentioned, but visually I assumed it was another ship simply because of the other people on board in the ship that you see post fly-by. As you said "Could Trinity have dragged Neo back to the Logos, returned to Zion for minor repairs and then all go out patrolling with Neo on board because they didn't feel much like dancing? Yeah I can handle that." You would think they would have dropped a severly wounded Neo off at Zion, not gone back out with him in a coma once Trinity returned to Zion. Those silly kids. That said I can handle it too.
The transition from the dancing was fine, although I'm going to stick to my guns that the dancing was about a minute too long

I'll be curious to see what you're going to do with the opening now without the voice over. Best of luck with that. I'm looking forward to seeing the next cut.