If you change your head unit you will need a device to interface with the steering controls. You lose some of the control; for instance I can choose to have mine wired to skip tracks when listening to the iPod OR change radio presets, but not both.
don't feed any more power to the stock sub. It probably can't handle it.
This is just my opinion, but I would go with the pioneer over the fosgate in a heartbeat. I've owned fosgate and to me the experience is, 'loud but dirty'.
If you want 12", it is most likely that you will need to go shallow mount subs, which can be spendy. Some may claim that they can get larger stuff in the truck, but you need to ask if they provided the right amount of airspace in the sub box, if the sub is slapping the back of the seat, or if they did some modding to the seat/install location. Making sure everything fits the way you want is key.
It seems that for what fits in our trucks, a single sub will want an average of 300w RMS. More power is better, don't be afraid to use a heftier amp (you can always turn down the gain).
wait on sound deadener. Unless you are messing with the doors, you may not need it as much as you think. I've been advised that most of the rattle would be from the rear window, and you really can't glue on sound deadener to that!

In mine, the only rattle I have so far is in either the glove box or passenger a-pillar. I will be doing sound deadening, but it's for the benefit of the door speakers. Leftover scraps will go to the back wall.
You will need at the very least:
amp
sub
sub box
18' of power wire (guage dependent on your setup)
5' or so of ground wire
fuse block or circuit breaker
crimp on ring terminals, etc.
a way to secure the amp (most likely an amp rack or under passenger seat)
speaker wire
I may be missing some stuff, but that's a good start for the checklist.