the $1000 challange is a good place to look for ideas. For front speakers, really just go listen to as many as you can put your ears on. I highly recommend components, and halfway decent ones at that. just take some music with you and go listen. there's ten billion things ppl can tell you and you can look up all the specs you want, but in the end, it's your ears and noone can tell you what they like. A good place to start is looking at $300ish components. JL, Focal, Boston, DLS, Image Dynamics, Diamond, (believe it or not kicker), MBquart (if you can find them still) etc are some brands to checkout. Also listne to them all as objectively as possible. often you'll find that more money does NOT alwas equal better sound. But the real key her eis to take some time and listen to speakers. make sure you have your own music with you so you've got familiar tunes and you cna really get into details. I actually have a couple of mix discs (all pure wav files that haven't been compressed to mp3 and back) that I take with me everywhere I go just in case. If a salesguy insists on bugging you, ask them if they can set everything flat and turn off everything but deck, amp and the speakers you're comparing so you can get a good ear for the speakers.
As far as your amp, YES the stock amp will work, many have done it, but it's a bit on the weak side. You might want to consider looking into just getting a good solid 4channel amp and running everything off of it. something rated say 75wRMS per channel will give you close to 250 or 300 bridged so you can run the front two stereo to your front speakers, then bridge the rears for your sub.
Currently I'm helping a friend put together a setup running infinity refrence components, a decent 12" sub, and
this amp. Oh, another note, don't limit yourself to 5x7 components. 6's and 5's can be made to fit with fairly little hassle.
with dynomat, trunk kind of, doors for sure front doors at least.
ghetto-rattle isn't necc stopped with dynomat, just helped. for that you
may have to do it the old fashon way, get some caulking, weatherstripping, and whatever other sorts of foam or rubber you can find to wedge between vibrating panels, etc.