I feel pretty safe saying this is definitely Shinji now.
If you look closely he's got a thread heading down from his upper body on the left side of him, which I'm thinking is the SDAT headphones.
I think it's just a pencil stroke due to the art style, if you looks closely there is a similar one on his right leg.
On the same vein, if you look at his neck, the black of the hair continue past the neck and to the right, like a ponytail, or again the color that overflows due to the art style.
Also, thanks to the immense zoom offered by the hosting site, I can say that the big structure looks like a giant launching bay for aircrafts : there is a row of ramps, each leading to a big door in a rectangular structure, maybe a hangar.
Also, if you look closely at the background at left of the walking character, you can distinguish a big structure with what looks like two chimney, or two towers.
So, about the other interesting ones :
That's actually a diagram of how the MAGI system works. At first I thought that it was WILLE's MAGI Achiral system, but upon closer inspection, turns out it's NERV's old System : there is a mention of a "NERV MAGI System" on the legend, and when you zoom at maximum on the center, the three red hexagon on the center have the label MELCHIOR, BALTHAZAR and GASPAR(from left to right)
Now, Sakura with her friend :
The label of the restaurant is illegible, and Sakura's friend definitively have a Misato vibe, both in the hair color and style!
Our dear friend Kaworu with his mysterious plugsuit :
First : the plugsuit's collar area is upturned, which with the lighting makes it impossible to say if it's the Mark.06 or EVA-13 plugsuit.
Two : Is that an entry plug port on his neck?!
The cylindric thing is definitively an entry plug.
Although it's probably just a trick of the perspective and there is an Eva hided by Kaworu's body.
The trio and the cat :
That's definitively Rei Q and Shinji's feet, and for some reason Asuka's feet is from her tapped up plugsuit form the first half of Q(probably a liberty taken by the artist so we could see it's Asuka, since her new plugsuit is black/dark purple at the feet)
Size comparison :
It's impossible to see without zooming, but the five person in the Japanese Navy uniforms are actually the five Eva pilots!
(Rei, Kaworu, Shinji, Asuka and Mari)