Welcome...so you snagged one from Quantico Arms...all but one of my lowers are Eagles. They work great!
Any upper will fit...I've used Armalite and Rock River, but any AR upper other than Colt will go right on...it's as simple as pulling the pins, mating up the upper and lower, and putting the pins in. If you're lucky, the pins will be tight, but not ridiculous. Even if they're loose, it won't effect function...and you can always use and Accu Wedge if you want.
For what you say you want, I'd recommend a 16" upper, maybe an M4 style. A complete RRA M4 upper with bolt group and chrome lining is $442 from ADCO, which includes shipping. I've got one, it's a very nice upper than has run smoothly since I got it.
As for sights, I went with the Holosight (poor man's Eotech) and an ARMS #40. The Holosight bolts right on the flat top, and allows a perfect co-witness with the ARMS # 40 BUIS. It's a perfect combo.
Here's my rig...it's got some extra stuff, but you get the drift:
[img]http://img.villagephotos.com/p/2003-5/188491/cqb1.jpg[/img]
close up of Holosight and ARMS # 40:
[img]http://img.villagephotos.com/p/2003-7/188491/flattop1.jpg[/img]
There are certainly other approaches to a CQB style rifle...but I really like the Holosight/Eotech reticle for close in...it's very easy to see. I've got an Aimpoint on my other shorty CQB style rifle, but prefer the Holosight.