lights are key. get the ones with quick release brackets so she can take them off when she locks up.

strip down the frame and leave it bare (if it's not steel) or krylon it flat black or something if it's steel. just make it look boring. that's easier than wrapping the frame in inner tubes, which will eventually come off, and is also easier to clean.

i'd definitely go with free as opposed to fixed (esp for a first time city rider)

you might consider a QR for the front wheel so she can remove it and lock it to the rear or take it with her, but she's gotta be vigilant about it.

maybe a rack for the rear to carry books/supplies.

as for the wheels, you're overdoing it for a 90lb girl who is not going to be riding agressively! i weigh 170 and beat the living hell out of my 32 spoke surley/ma3 wheels and they're doing just fine. i true them now and then, sure, but i also skid left and right and ride over some pretty horrible terrain down in dumbo (where cobblestone streets abound....)

yes, there are pot holes, but you can steer around them pretty easily at slower speeds. the roads, esp in manhattan, aren't *that bad*. some of you sound like riding in manhattan involves climbing mountains of smashed glass and nails.

the chain on the saddle is essential, and two brake cables coming from the bars are a good way to help prevent stem/bar theft (i've had several friends have their stems and bars stolen - pretty easy to do by losening one bolt in most cases, esp when it's a track bike with no levers).

use flat (and relatively narrow) bars for sure. a novice cyclist won't use drops or bar ends.

use loctite on everything possible.

armadillo tires are in order.

make sure she has a pump and knows how to change tubes and inflate tires.

there's a bike shop on lafayette st, just a few blocks from her school, called bicycle habitat. they are just awesome and friendly people and deal a lot with fixies and city bikes and will totall help her out if she needs it.