A couple of quick comments (my two cents, take it or leave it as you will)
"Blue - Orange contact!" "Confirmed!" Two unfamiliar men said.
"Confirmed!" two unfamiliar men said.
-->Do not capitalize after a quote, if you are continuing the sentence.
Also, I would've split this up a bit:
"Blue - Orange contact!" announced an unfamiliar voice.
"Confirmed!" replied someone else.
...or something like that.
I wrapped around Rei and even behind a building with my eyes shut tight and
my body wrapped around my head I could see a bright flash.
"Brother, brother, where are you?" A half mile away from Shinji, a young
girl looked up from the rubble of an apartment complex and into the light
of a thousand suns.
We bounced for several seconds then we stopped and I looked back, "Did we
get it?"
Okay, this doesn't work. You have been writing from Shinji's point of view for the whole thing, then you abruptly switch focus for two sentences, and then switch back. It's jarring, and throws off any flow you have built up until this point.
The only way I can think of to fix this is to have the girl be closer, and Shinji hear (but not register) what she said. Either that, or re-write the whole thing in 3rd person omniscient, but that'd be rather drastic.
Again, just my two cents.