Disclaimer: This is information is based solely from my experience/knowledge. I am not now nor have I ever been a professional audio installer, but I get by. :)
Borrowing from another thread, take your time and do a bit of research. I have a truck similar to yours ('00 Supercab) and am doing the same thing now. I already have a few components and will be slowly adding more as $$ is more available (when I sell my ghia). The idea of an aftermarket HU is a good one and the one you mention looks to be a pretty good start. A 4ch amplifier is also the route I will eventually be taking after better speakers are added. The AP740
that I've seen looks like a pretty good choice to me. I myself have only an old alpine F240 with 40W/ch. I've found that it is more than enough power for what I will be picking up for the main speakers.
Speaking of speakers, my plan is to go with what fits in the stock location simply to eliminate extra headaches of hacking apart the truck anymore than is necessary. True, 6x9's will give better bass response than 6x8/5x7's, but if you're adding a sub in the rear, that won't really matter in the grand scheme of things. It just won't be worth the time/effort/swearing/bloodied knuckles of grinding away metal to make something fit. (Plus, it opens to path for unwanted rattles in certain cases.) My suggestion would be to get a set of (stock sized) speakers that you like for up front. The best ones that you can afford (ie. seperates or really good 3/4-way) should go up front as this helps set up for a really sound stage if you prefer to listen to your music from the front. (If you prefer to listen with the music behind you, reverse the ideas I'm showing you.) I've found that adding a decent set of coax or 3-way in the back will do just fine. Something with decent mids and highs should do the trick. You don't have to throw big money into these unless you want to. I will most likely be buying a cheaper set for the rear and I may even leave the stock ones back there for a while (since nobody sits back there anyway.) Get an amplifier that matches these speakers in the power department. You can get really solid sound from a 40W/ch amp and speakers that are matched for it. Remember the stock sound system does 'ok', and it probably has no more than 20w/ch if that.
As for the sub, this is the problem that I am currently working on. If you you are using the read for storage (like I am), you might want to go with something smaller. If you can spare the space, you are limited only by your imagination and bank account. My plans are either a) two 8's sealed and tucked into the corners (my seats are removed, I don't need them) or a single 10 also sealed behind the drivers seat. Ported or sealed is your choice. ported= lower bass response and better 'slam' and less power required, while sealed = tighter more controlled bass within a smaller space, but needs more power. (I had a 10" Solobaric in a tight sealed box with 500W on it and it took it all. It's currently in my brother-in-laws truck. Now I wish I hadn't traded it...) The choice is yours but in previous years, I've gone with sealed boxes and have been happy as a clam. On the other hand a friend of mine has 2 8" Audiobahns in a ported enclosure in his Colorado and they get low and loud. And again, find a driver(s) that matches your amplifier or vice versa. If you can afford it, find a 5/6 ch amp that will power all of it at one go. (Wish I'd done this a while ago.) This makes amp mounting easier as you've got only one to deal with.
Hope this info helps. Looks like you've already got a few good ideas. Good luck with your setup!