Holy crap man, that could take a book to answer!!
*heh* Ah well, alas maybe helping you will shed some light on my dilema so here goes....From the top....
Sound quality is alot harder to get the loud. You have to take into account imaging and staging. The "ideal" (Per competition standards) setup is to mimic concert cound. Thus, everything should appear to come from in front of you, as if you were in the center of an orchestra. You would hear things positioned as they would be on the stage, slightly above eye level strings on left drums on right or however it *should* be in real life. But, we're not competeing and you may not even like that. But, to that end rear fill is a huge no no. Thus, you'd onyl want mids and highs coming from the front. I've heard you can get midbass in the back, but thats master installer kind of stuff. I havent tried it yet but I'm going to.
Moving on. $1000 is a decent budget if your willing to shop online. I would imagine so, but going to B&M stores with that and you'll get eaten alive FAST. Install is really gonna vary depending how in depth you go. Replace factory stock locations with drop in replacements and no dampening and it should be fairly reasonable. Get even a bit custom and I could see half that budget going up in install. May wanna think of doing some or most yourself, its really not all that hard (Except door panels. Damn I hate door panels)
The HU, while not a top end killer, will do the job. What kind of outputs does it have? Hopefully 3, Front / Rear / Mono (bass). Hopefully at LEAST 2 volts out.
I agree with the same brands to an extent. I like to keep amps the same and speakers the same. Really, unless you advertise what they are people wouldnt really know, and diversifying allows you to get the best of what a company has to offer.
And now the fun part! Selection. Infinity is good stuff for sure. You wont go wrong with it, although its not MY first choice. Have you demo'd them? I'll be frank, bass is bass. It'll sound nearly the same from a Jensen or a W7. Find something you like and go with it. Now, move up from the bass and its a whole new ball game. Mids and highs speakers each have there own sound. And every damned on sounds different. So, that makes it difficult to recommend a component / coax set that you would like. Its something that really is better off if you can go actually hear them. I personally really like the JL Audio XR series components. I also like the Infinity Kappa Perfects. Alot of brands have a very bright tweeter. Focal and MB Quart have REALLY bright tweeters. If you like blazing highs, look into those for sure. They dont sound bad, they arent ditorted, there just VERY bright. Not so much my taste, thus I dont, and probably wouldnt use them. But, Focal is also generally regarded as one of, if not thee, best component set money can buy. The top end weighs in around $1500 bucks. So, to say they have bright tweeters is not to imply they have bad. Thats just to show every speaker sounds a bit different.
Amps are kinda more depentdent on budget then anything. Amps, like speakers, can run from pretty affordable up to insane. Sinfoni and Brax coem to mind. Lets just say i cant think of 1 amp in their entire lineup you could get with $1000. No, I dont run them but I would like to

JBL is an excellent "bang for the buck" amp. Online JL audio is good as well, Visionik, Power Acoustics is alright. Basically, all amps sound the same. The reason people say amps sound different is due to the added features such as crossovers and bass boosts. So, find an amp that gives you the power you need at a price you can afford. I personally dont like the all in one amps (The 5 channels and such) although thats personal preference. In a case such as yours, it may be the perfect fit. Again, personal preference.
You'll want 1 channel per side of the car. Thus, 1 channel for the front right, 1 for front left, 1 for rear right etc. Also, 1 channel for the sub. Components and Coax's, although using mulitple speakers, all run from 1 channel. You could do a 5 channel amp which would give you 2 fronts for the doors, 2 rear channels for the deck and 1 sub channel. I think my biggest complaint is they dont have enough oomph on the sub output for me. I need 1000 watts to really get my sub to stand up and shine, and the most I think I've EVER seen is around 300. You could also get 2 amps, either a 2 channel or 4 channel for mids n highs and a mono amp for the sub. I would go that route, although that does add to install cost but allows a bit more flexability. Advantages either way.
For power, just find the RMS of your speaker. Find an amp that puts out at least 1 watt but not more then about 25% over the RMS rating. Use that and you'll be fine. Thus, if you get a component set that has an RMS of 100 watts, find an amp that gives around 50-125 watts per channel. Yes, you *can* do more, but I dont recommend running alot of power if your not a fairly experienced user. Its important to realize when your speakers are reaching their limits, and some cant do that. And no, underpowering wont hurt them. Clipping of the amp does. We'll go into that later if needed.
Now the features. Crossover. Think of this as a router. We have 20-20,000 frequencies. Well, the crossover just routes them where they should go. Thus, a high pass (HP) crossover set to 1000 will allow any frequency of 1000 hertz or greater to pass. Anything else and it blocks it (It actually attenuates it...) Each channel of an amp refers to an output section. 2 channel, 2 outputs. most amps rate power per channelx channels...ie...100x2 = 100 watts on each channel, 2 channels. This would be able to run component sets, coax's or whatever else. Bridged is combining our channels for mroe power. Our 100x2 amp? Bridge it and it (may) go to 200x1. Twice the power, only 1 output (Channel) Generally used for sub applications, or to bridge a 4 channel to 2 channel for more power on some mids and highs.
The crossover is important in that we want to route our signals to the right place. We dont want subs playing vocals, and dont want tweets playing bass. Thats why there there.
Caps. No. I wouldnt advise one. Waste of money in my opinion. Thats all i will say there.
I would buy online. You can save alot of money. Example... I went to listen to some JL XR 650CSi (Top end 2 ways) They wanted 400 in the store. I found them online for 250. Well, that give me an etra 150 to either step up to a higher model (The 3 ways) or to put towards an amp.
So, now lets peice out an example system.....This will actually be flavored more for me, so you wont see rear fill......
JL XR 650CSi = 259 (I prefer components over coax, it wont matter much excpet coax is eaiser to install)
JL 300/2 Amp = 329
That would take care of your mids and highs in a very nice way. Keep in mind, those XR's are the top of the line JL components. You can drop to a lowe rline or a different brand and cut some money.
Here is some Infinity Kappa components for $179. Really thats up to you.
Next is the sub. First off, I cant stress this enough.Listen
Carefully.
I mean it!!
Speaker size does not affect sound quality
Yes, a 10" is as "tight", "rich", "quick", "responsive", "signals aliens" or whatever else people say as a 12 or a 15" speaker. Install and how the speaker was designed are what determines this!!
With that being said, I'm recommending you a 12".
Adire Shiva
I dont think you can find a better 12" speaker on the market for the price. I also think you;d be hard pressed to find as good of one for even twice the money. I havent heard it personally, but I;ve heard alot, I mean ALOT of good about it. And now the amp! So, sticking with JL....
JL 500/1 = 400
So, that would round you out at 1100 bucks, less install. Again though, dropping those JL XR's for a lesser line would help out alot. But, if I were you and wanted to cut some bucks from there I'd look elsewhere for amps. Lets redo it using JBL amps. Still good amps, and alot less....
JBL 180.2 = 170 (For your components)
JBL 600.1 = 260 (For the sub)
That takes total cost of amps from 729 down to 450 or so. Hell of a drop eh?
Hope that gets you started, if you have any other questions just ask away.
(No, that didnt solve my problem...damn the luck...)