I had one more possible thought for having a visual of Neo getting picked up at the machine city. There is a over head shot of Neo and Trinity's ship flying over three powerlines real slow right before they get attacked approaching Machine City. It's at 1:01:26 - 1:01:30 in your version. If you have the Animatrix outside ship shot and then moved the overhead shot after it, it might work. Not sure but its a thought.

You could also cut from the dancing/celebration to trinity holding neo's hand in the coma. After trinity says "I'm staying with him" and the nurse leaves then show the ship flying over the power lines (or your orginal fly-by) followed by a cut to Morpheus saying lets look for Neo in the matrix. Might make it flow better, might not. Hope this helps in some way.