I agree with a lot of what you've said and some of it is already taken care of, some I tried to convince myself was ok (even though I knew it wasn't).
Rethinking the opening with Neo looking for the Oracle, I've decided there isn't enough action to open the film, so I'll go back to the Seraph one.
I'm also going to move the hall scene (looking for the Oracle) to after Neo jacks in so we have a better explaination why he's gone in.
The extended jack in... check, if you blinked you missed the old one.
Trim the rave? Possibly, I haven't sat through it straight though in awhile so I haven't judged the pace, but it's likely to happen (sweaty dreadlock guy is first to go
).I really intended to give the impression that you might actually be seeing the Logos at the end (Trinity would have brought Neo home) since the Hammer was seriously banged up (but the Logos only took moderate damage in my edit). But I actually like the idea of giving the impression that they went to retrieve Neo and Trinity in a hastily patched up Hammer... hmmm. I'll have to think about that.
Btw, would you be able to play a KVCD instead of Xvid? It's just a variation on the VCD standard, optimized for better quality and some filtering to improve compressibility. It's not 100% compatible with the VCD spec, but most stand alone DVD players are fine with it. It would also mean no one would have sync issues.
As far as the abruptness of the jack-in the only thing useful I found was Morpheus saying "The Oracle must be consulted" from M2, but he's using his speech voice so it sounds out of place. Hence I figure just showing him looking for the Oracle may fill the lack of audio explaination.