I'll post some decent scans at a later point. (I'm at home now, and my scanner here is small and covered in old clothes and dust.)
- Misato's 2I flashback montage had a cut at the end showing blood squirting from the South Pole and reaching the Moon (see linked thread)
- The scene with Rei's mysterious underground facility was longer. Her visit to the oversized test tube was prefaced by a stop with Ritsuko at another facility (consisting of a bunch of large pillars in a pit, in a blatantly SToL-like configuration) where Rei is showering after doing something mysterious.
- The scenes with Shinji watching Rei wring out a cloth and embarrassing her in the elevator are present.
- Eva-04 would have been shown in the report Fuyutsuki was holding.
- During Asuka's Eva-03 test: She doesn't sprout "wings" (but she's still flung forward the same way). Instead of "feathers" flocking toward her, it's a bunch of NEEDLES.
- After her face is struck by the needles, there's a chopped scene (which most people have already heard about; there are pics and translations around here somewhere) where her face gets ripped off and talks to her in Kaworu's voice. Asuka ends up pulling her face back on and being surrounded by big needly things, "like a porcupine".
- 9th Angel's explosion makes a giant tree-shaped thing.
- When Shinji checks out Eva-03's entry plug, a bunch of faces or something form out of the Bardi-goo.
- Before the cut where Eva-01 punches in Eva-03's face: Eva-03's upper body tries to crawl away, but gets grabbed and violently slammed into the ground again. (That sounds so awesomely grisly; I hate that this was cut.) In the dialogue column, "(Asuka)" is written next to the sound Eva-03 makes as it tries to escape.
- The scene where Shinji sees Eva-03's pilot extracted from the plug was present. (Basically the same as the Toji version, just with Asuka in there instead.)
- There is a cut Seele dialogue after this where they say stuff about Angels merging with humans or whatever. (I think it's meant to anticipate the 10th Angel, similar to how the Seele dialogue in #17 anticipated future Angel-human contact.)
- Scene with Kensuke trying to call Shinji after he quits is present.
- Right after 10th Angel grows a humanoid body, there was a cut of the core "becoming a person's face". (Really scribbly; all I can see is the lower half of a face with a Viral-esque slasher smirk.) Dialogue column here says "groaning sounds (voice same as Rei's)". [However, the core looks perfectly normal later...]
- The dummy system was originally labeled "Rei-00". The sound that comes out of the entry plug when Eva-01 rejects it is said to be "like Rei screaming" in the storyboard, and just "like screaming" in the script. (The stuff about the DMYSYS being from Golgotha IS here, BTW.)
- After 10th barges into the command center, a bunch of pillars pop out of the floor in front of the command tower. (Angel-sealing hex pillars, maybe?) Looks like Zer starts chargin' its lazers anyway.
- Giant red Rei is tentatively drawn as having a core (right below the clavicles; whatever happened to solar plexus love?).
- Eva-01 sort of wraps its right arm around Rei and pushes her in, instead of just floating there while she sinks in.
- The cut with the cross-shaped incision doesn't have any vortex forming above it. This is delayed until the next cut (the close-up of the ground being sucked toward the sky), where a big vortex is opening above a little vortex, and the big one eventually develops a black hole. The description refers to this as a "door opening". (c.f. the original publicity poster's reference to a "door")
- Right after Eva-01 becomes a glowy thing, Maya was going to hectically squeal something about synch ratio surpassing something and something-something two A.T. Fields merging not-believable.
Okay, that's it for now.