For the opening I perfer the original one as you did, it's not perfect but I think it works better then the other clip I saw and I actually think it works well to set up whats happening. I still think it has a nice ominous feel for the opening of the film.
In terms of Neo jacking in right before he fights Smith, I saw you used a second or two from Reloaded to show him jacking in, but even though I knew it was Neo jackin in, I though there might be a clearer shot of his face when he jacks in. But for me I just think the dialog works better with what I posted earlier then everyone talking about the looking for the Logos before the M3 Smith fight. It sets up that there is something wrong with the matrix before Neo goes in to fight Smith (i'm just going to cut and paste this from my previous post cause I'm lazy)
"the 10 seconds from the original Revolutions from 43:36 "There's something wrong with the Matrix" to 43:46 "This can't be good". This footage would be inserted right after the end of the shot with Evil Bane on the table in a coma and lead into the shot of Neo jacking in to the Matrix. That ten seconds of dialouge makes it sound like Smith has overtaken the Matrix so it fits well right before the fight with Agent Smith." This is already convienent because you had already cut the original 10 seconds I mention here out of your cut so you can use it without reporposeing anything. To me it fits the the setup a little neater and I think it might work well with your idea of moving the hallway sceen as well.I'm glad you liked the idea of the Hammer picking them up at the end. It would be sorta implied that its the Hammer, but to me one of the first things that happens when peace is declared in war is that you get to pick up you dead and wounded, so I think it kinda fits and it shows the war is truly over.
Hope all is going well.