DR3W, this is the thought process I put into a lot of things I do for the Expy. But, this is what has also allowed me to get my Expy to where it is.
With that being said, I recommend the following sequence of questions/answers as this will give you a logical flow of questions and answers without having to go back and relook at things.
-determine how much you are wanting to spend and how much power you are wanting
-get a rough idea of how much power is going to be needed at each speaker. The rule of thumb I use is to take your total power, divide it first in half (mids/tweets and subs). Take the sub power and divide it by the number of subs you have. Take the mid/tweet power and divide that by 4 (for each corner of the truck). Now you have your power requirements for what the radio may need to put out, the speakers need to be able to handle, and if you are using external amps, what power those need to make.
-determine the headunit that you want, get down to the model, specs, etc Make sure that if you are using the head unit power, that it is capable of outputting the power you are wanting (power = volume for the most part, more on this later).
-figure out the speakers you want, their specs and ensure that they can handle at least the power you are looking to run (if using the factory speakers, this may dictate some other things, so, keep that in mind, any questions, ask). One number I recommend you write down is the "sensitivity" of each speaker. In short, you want all the speakers to be as close in sensitivity as possible. Odds are they won't be and don't let this limit your selection, but additional changes may be needed to account for this. Normally subs run 2-4 dB/W less in sensitivity than mids/tweets, but don't fret, I will show you how to get around this (its easy). I also tend to recommend getting speakers with slightly higher sensitivity for the front speakers as compared to the rear speakers for the mids/tweets. Why you ask? This helps keep the staging more towards the front of the truck which is the sound style that most people like. If you are wanting a center stage feel (ie, like you are sitting in the middle of the band), then getting speakers with the exact same sensitivity is more important.
-Now that you have your speakers, find amps that meet your power needs and also run the frequency spectrum that you needing. If putting in an amp for the mids/tweets, you want an amp that goes from at least 20-20K Hz. For the sub amp, you really only need an amp that will output from 15-200 Hz. But, you will find that most of them will do 20-20K Hz. I would also recommend getting amp(s) with built in cross-overs. This will make the system easier to install. Keep in mind, you will need to limit the maximum frequency of the sub to some level and need the mids/tweets to take over at that same level. So, the crossovers need to be able to meet somewhere. I personally like to run my subs up to a higher frequency that most (in your case, I say 180-200 HZ), but you will find others that will recommend crossing over at around 100 Hz. The higher frequencies tend to work better for country and rock, but lower for Rap and ultrabass stuff. There is no single "correct answer". Like I mentioned earlier, you may need to adjust the power going to any speaker, find the speaker with the highest sensitivity and then find the difference in the sensitivity (front speakers are 89 dB, subs are 86 dB for example, for a difference of 3dB). The rule of thumb is for every 3 dB, you need to double the power. So, in the case of subs, if you determined that you needed 100 W for each sub, but they are 3dB less sensitive, then you need to run 200W to the subs (just make sure that this new power matches what the subs are capable of handling). Worst case, get an amp that is slightly over what you are needing as you can always turn it down with no problems, but you can't turn it up.
-finally, now that you have all your components, you need to pick the wiring to make this all work. If you need to skimp somewhere, THIS IS NOT THE PLACE!!!!!!!!! I can make a smaller amp sound much bigger than it is by using the proper wiring and vice versa, using the wrong wiring, a large amp can sound very small. With this being said, you don't have to blow big money for high end cable. From the speakers back to what is powering them, stick with some 14 gauge speaker wire. For the wires running to the amp(s), 6 gauge at a minimum (for up to 500 W RMS), 4 gauge (possibly bigger) for larger systems. You can find kits that sell for $30 that will have a lot of what you are after. You buy the wire by the foot and it will easily exceed that based on the prices that they normally ask. So, do some looking around and look on E-bay as they have the kits for dirty cheap there. I also recommend soldering the wires to the speakers to ensure the best connection possible (no sense in letting the sound power go up in heat due to high resistance connections). Plan on spending about $100 on wiring, connectors, fuses, etc.
That should get you going on selecting components and what not. If you are going to buy new mid/tweets, I have a thought process for that too and if you want to hear it, I will pass it on.
I know this seems like information overload, but, once you get into it, you will see how the options will be limited for you based on what you have selected. You may also want to take a step or two back and make a change to give you what you are after. Having a piece of paper and writing things down is also very helpful. I normally draw a large rectangle, label the top "front bumper", the bottom rear bumper, and then I start drawing in boxes (for radio, amps, etc) and circles (speakers) so I can get an idea of where the components are going, what models I am looking at, and some key information about the components. That way, all your information is in one spot.
As for picking components, it is like a fart, everyone has them, but they all tend to stink. But, in short, you will get what you pay for. So, do a lot of looking and figure out what you are willing to spend. That may also dictate what you do and do not get. Sticking with brand names normally is a good place to start, but some of the no name stuff can be good too.
One final thing, when looking at specs, make sure that you are comparing apples to apples. This is especially true with amp power. Compare W RMS to W RMS. If they only say the amp/radio outputs XX watts, they are talking peak watts. To be able to convert that over to say RMS watts (W RMS), divide the peak power by two. This will help keep things on a level playing field. Peak power don't mean squat, try to keep everything on the W RMS scale.