Hmm. The rotoscope of the blind fold clips sounds good, and it will really only be brief. I actually stand a chance of cropping the scene if I can't find anyone to help. Sloppy but it'll do the job.
The first Matrix will be untouched. I find it to be a nearly perfect movie.
The second will actually have fewer (drastic) changes than the third. I'll attempt to improve the 2nd but the problem is there's little you can do with what is there. The Dezionized people showed me a lot of good ideas, but short of cutting slow parts, I'm not sure it can be made a lot better.
When I'm done you'll probably rate the movies from best to worst as M1, M3, M2 (which in my mind reverses the order of the last 2 films.)
The worst problem is that the second movie lacked any real subtext. The third at least attempted to incorporate religious allusions to the story like the original. The second is just a mindless thrill ride and little else.
As far as Agent code. I think that can be explained away because agents after the first film are version 2.0 (according to credits). Neo even comments on the upgrades. New code could be a new color.