I am aware that some music transitions might have been sloppy, but under the circumstances I found few alternatives and had to settle for preventing real abrupt cuts. I'm sure there's a better way, maybe resyncing the soundtrack, but there's no way I'm going to try that any further (I did at 2 points in Revolutions).

Can you elaborate on the "silences?"

As for the Oracle scene, yup, rickety as hell. I made sure that the audio from Smith never stops or fades but is continuous even across the Oracle's clips. This was to allow any ambient sounds to overlay her dialog. I gotta say, except for the localization problem I'm not sure I hear what you do.

As far as Link missing the call I'm not sure I'd call it that. It was a creative decision for the transition. I noticed the CBB version had Trinity pick up the phone but not dial, the next audio is the ringing for Link who answers.
I liked Trinity dialing in the Matrix and Link answering in TRW. To keep the full audio for Link involves a ringing in the Matrix and again in TRW which is in too brief a span to be natural sounding.

I guess my bigger concern with the edit is any pops or techinical problems.

The funny thing is, your exceptions with this are largely the things I thought I got right.
I will tell you if you found the movie to lack fluidity, stay away from M3. It is definitely a rough cut more for the impression of what the movie could have been than a good movie experience.