A true SQ setup is something very different than you had in mind. You're fine for the hardware you have now, but your ideas about where to go next is way off.
Put the Alpine Type-R 6.5" set in the front doors or kick panels. Run the tweeter down by the woofer or in the a-pillar(firing slightly up and back towards you). I think the Type-R tweeters are on a swivel cup that will let you adjust and point anywhere that works well but I'm not sure. If not, you'll have to aim appropriately when you install. The Type-R is not a bad set actually. It may lack a little in overall detail, but the warm and smooth nature and good tonality is nice. I've always enjoyed them myself and would even run a set over Morel, but that's really a matter of taste.
You have a TON of speaker choices, and it will primarily come up to personal preference, and your wallet.//content.invisioncic.com/y282845/emoticons/laugh.gif.48439b2acf2cfca21620f01e7f77d1e4.gif
My suggestion for the sub is to not use JL's specs. Model up the woofer in box building software or Excel spreadsheet(lots of these tools available online). Go ported, and build to "ideal" spec. This will notably be larger and tuned lower than what JL suggests, however, it will provide a flat and more extended frequency response which is generally desired in SQ.
You will not find good 6x9 woofers nor 4" component sets. They just are not made and very few, good options are available. You're pretty much stuck with 5.25" and 6.5" sets. Since you have the Alpine's already, just use them for now.
With a subwoofer in the trunk, do NOT put 6x9 speakers in the rear deck. Even take out the stock ones if they are still there. The sub will push and pull on the 6x9s and just make them distort horribly. In order to make use of a pair of 6x9 speakers in the rear deck, you pretty much have to build a box around them and seal them off from the rest of the trunk.
Then there's the issue of rear fill. When talking about SQ, refill is generally considered a bad thing. Ideally, audio is a 2 channel setup. You have a left, a right, and a blending of the two to make everything in between. This left, right, and middle area creates your sound stage. When done well, you can actually "see" the music in front of you. You can mentally see locations of the performers, where the drum sits, where the bass guitar player is standing, where the singer is, and you can even see depth. This is the perception of a "physical" music stage in front of you. Creating a good sound stage is a main goal of a SQ setup. Music is developed as two channels and should be presented in only 2 channels. You should have a single left source and a single right source, and that's it. Adding more sources just messes things up. It's like having two stereos in one room and playing them both at the same time. It gets mess, potentially very messy. The only real gain is loudness, but in the process, you destroy the sound stage.
Subwoofers, as long as they are crossed low enough, do not take major part in this sound stage reproduction. Low bass is omnidirectional. It's present, but you can't mentally define location.
The Cleansweep is an option. However, for the same price you could buy yourself a very nice HU. You'll have to decide what route you want to go as far as HU/processing goes. Also consider what features these options provide and if you even need all of them or desire more. When you're done, you're stuck with what you've got, so make sure it's enough for now and for any future plans.
ECA has a few good tutorials discussing the concepts and goals behind sound quality:
http://www.elitecaraudio.com/search.php?query=&topic=1/
I will also state that you do NOT need expensive speakers to sound good, just a good(smart) install and good tuning. This is why I tell you to stay with the Type-R components. Unless you are looking for a different sound or need to step beyond their performance/capability level, there's no reason to change. Most everything else can be taken care of through installation and tuning. The same applies for the sub. Stick with it unless you are looking for something different in sound or capability that can't be achieved through install/box configuration/tuning.
Invest in deadening. Set a good chunk of the budget aside for this as it will be very benificial to the end result, especially with noisy, rattle happy cars. Unless you're running a high end Lexus or Mercedes or something that's hugely deadened from the factory, there's a lot of room to gain here.