I've been doing custom installs for years and with my own truck I went pretty mild and love it. I agree with spending a little more and having it last though. When I did my install on my 99' ext cab, I gutted it and ran all new wires, etc. However that's not something you NEED to do. I was just bored and figured why not. One component I would absolutely recommend if NOTHING else, would be the QLogic Custom Enclosure for your truck. I cringed when I hit the "Buy" button when I first got it, so know that it's going to seem pretty pricey for a box. However I can honestly say that it's the best part of my system and I'm glad I bought one.
Since mine is the Ext Cab and not the Super Cab, the box is a downfire type, sealed box that creates a nice center counsel for the rear bench. The big thing is that it's TUNED by QLogic to the type of sub that you can put in there. Sure there is a WIDE range of subs you can install in it, but the ones that will fit are going to be all designed to work with a certain air space requirement. And Qlogic went and designed the enclosure to get the most bang for your buck.
I'm running an entry level JL 10" sub and only maybe a 200w amp and when I want it to pound, it will. However for everyday use, I turn it down a bit and it compliments anything I'm listening to VERY nicely.
Now here's another little tip. I'm running Alpine 6x9's in all the doors with a Alpine headunit. I'm doing that instead of mixing and matching because they are designed and tested to work together. The same goes with JVC, Pioneer, Fosgate, etc... So I would suggest you buy all the same of one brand, whatever that may end up being, rather than winging it. Alpine for example tests and manufactures it's products in house and they are tuned and MADE to compliment each other. Where mixing Head units with drivers, you run the risk of conflicting freq's or massive power draw from a weak headunit trying to push a underpowered driver, etc.
Also another thing is get the baffles for the doors. They're made of poly-foam and keep the outside elements OUT of your speakers. Other than running to much power to them, the leading cause I've found for speakers crapping out, is that the dust and rain seeps into the empty space of your door and breaks down the speaker surrounds and clog the magnet journal. Then your left with a speaker that sounds like crap before it just dies. The baffles will cost you a whopping 5 or 6 dollars and will save you SO much headache later in life.
I've dealt with Crutchfield for years and frequently send people there, that are looking to build a system from scratch. What I do is input my vehicle and then it makes sure everything you can choose from, will indeed fit. Then once I've shopped around and found what I want, I open up a new window and start hunting. Basically having them do all the hard work of designing the system, then going elsewhere to find the speakers cheaper. Although a lot of the time I end up going back to Crutchfield to complete my order just for the info they include and their warranty alone. But at least you have that option if you can't find the components cheaper, elsewhere.
Anyway hope that helped with putting you on the right track. I did this all professionally so I'm just trying to give you a NO-BS answer. Because you go to a stereo shop and they're motivated to sell you what they have in OVERstock and not what is RIGHT for you. Anyway good luck.