I don't know if it's loo late for this, but I'd have a few suggestions for a final version:
-In Neo's dialogue with the Architect, there is one strongly noticable cut at 2:32 before the sentence "She would undoubtably be it's mother." He speaks of an "intuitive program" earlier, so "it" would refer to this program, rather than the matrix as in the original dialogue, where he refers to himself as the father of the matrix.
-Just before this scene, when Neo confronts the Source in Matrix Revolutions, there is a bit of dialogue:
<Neo: I only ask to say what I've come to say. After that you can do what you want, and I won't try and stop you.
Deus Ex Machina: Speak.">
This, together with Neo being plugged in, could serve as a good transition to the dialogue with the Architect
-At the very end (don't want to spoil it) how about letting the piano break from Rob D's "Clubbed to Death" play from the speakers? It's a very emotional piece and would also serve as a tie in with the music from part 1. And the transition to the credits would be perfect (with the beats kicking in when the screen goes black)