Thanks for chiming in!
I might like you, do this in stages. Head unit and speakers first.. and then later add the JL sub and amp the door speakers. This is all so expensive!!
I will also do the adapter so my steering wheel controls work.. I use them a lot.
If it were me and i was trying to do this on a budget i would do it in 3-4 parts, with part 4 being optional.
Part 1, replace the radio, install the pac harness and that will get your working for right now with steering wheel controls. I would still bypass the bose amp as discussed earlier in this thread. The aftermarket radio puts out the same power roughly as the bose amp (its within a few watts, and its more than half the power so theres no audible difference). That way you dont have any issues with the amp failing and your ready for further steps. You should also replace the speakers in this step if you can, these 2 things will make the largest improvement in audio quality in your truck.
Part 2, install the sub amp, power wire kit, capacitor should you choose to then install the sub amp and the sub box. This is the next largest improvement in audio quality
Part 3, install the 4 channel amp. This is the least benificial step in terms of over all audio quality, especially if you dont intend to crank it up. Note that something like the alpine powerpack might also be a good option for you since your not trying to win a soundoff competition.
Part 4 (optional), the last thing that you can do to improve the sound quality past this point is to reduce ambient noise and vibration. This gets expensive quickly. This step would entail adding Dynamat or the like to the doors, floors, roof, rear cab wall and then dynapad over some of that. The purpose of Dynamat and similar products is to add weight to the panels. The panel is going to vibrate, there is no stopping that, but if you add mass to it, it lowers the frequency of the vibration and if you add enough mass to it, it will drop it below the audible threshold for our hearing. The dynapad is there to keep the plastic door panels from buzzing against the metal (loose clips and such) as well as to keep the wire harnesses from making noise. It also reduces engine, road and air noise inside the cab which effectively adds power to your audio system.
Say that your ambient noise is 70 dB and your system can produce 90 dB. If it takes 100 amps to generate that 90 dB, then it will take 200 amps to generate 93 dB, 400 amps to generate 96 dB and so on. However, if you were to add dynamat to the truck and lower the ambient noise to 61 dB, you would effectively add the perceived audio power of 600 amps more input power with no extra load on the charging system. This too has diminishing returns though, you can only add so much mat in the truck, and adding more on top of that does not change anything significantly but the weight of your wallet.
Typically, i consider there to be 3 levels of sound damping installation
first, you buy a single door kit (usually like 4 sheets) and you cut them up into strips, and place them in key areas that are prone to flexing (the inside of the exterior sheet metal of the door for example, and the interior metal that supports the speaker. This is your best bang for the buck option, your maybe 100$ in materials and you get a good improvement in audio quality.
Next would be to cover every sheet metal surface in a layer of dynamat, i think this is excessive, and very expensive as your probably looking at close to 1500$ in materials to do it, but it does offer better noise reduction than just doing the strips. That said, you do not get a 15X improvement in audio quality, where as you do get a 15X increase in price.
Lastly would be to add dynapad over the mat, this is the final step and is one of the things that separates a "luxury" vehicle from a commuter. Adding a layer of this to all the interior panels will really quite the trucks ride down. The padding though is quite expensive as well so all said and done, it would not be unheard of to spend 2-3 K on sound damping. Personally, unless you have a hookup that can get you cost on the materials i would do the first option with some strips in strategic locations. This is a really good way to improve sound quality without breaking the bank, and you can always add more later.
a warning though on dynamat and pad and similar products (its more or less all the same stuff...) you do NOT want to put it over wire harnesses. That is to say that your dynamat should be atatched ONLY to sheet metal, and should not cover any wire harnesses. It wont hurt them, but if you ever need to get in there to replace something or need to get that harness out for any reason you will invent profanity never before imagined. Once bonded, dynamat is essentially forever, it is not meant to come off, even if baked in the Arizona sun. The pad is less of an issue, however what i like to do is put a strip under the harness, and a strip on the plastic door panel so that the harness is uncovered but sandwiched between the foam when the panels on. Ive been on the receiving end of a bad dynamat job where you have to dig wires out, i can tell you from experience that your bill will go up drastically if someone has to dig through that mess.