Hi BigKahuna, welcome to the club!
Keeping the stock head unit is no problem at all with the use of a line output converter, so that you'll have RCA outputs from the deck to input into your amps. People will start the usual "aftermarket sounds better", but that is an unfounded claim and keeping the factory head unit can save you money in two ways, since you'll save the cost of a new deck and not need various interfaces and adapters.
I would personally replace the front door speakers first; the replacements picked will depend upon your goals and uses. For a good upgrade that will vastly improve your daily driving experience without breaking the bank, just put in a set of high quality coaxials. You could spend more and put in components, but with the tweeter right beside the woofer, you'd basically have a coaxial anyway, just at a higher cost and install rate. If you like to experiment for the best image, the separate set would allow you to move the tweeter around, being the only true advantage.
You'll find sub boxes of all sorts on the pages of this forum. We've had everything from simple boxes that will hold a single 8" sub under the seat to midgates with enclosures built into them. Look around and see what you can find. It will all depend upon your needs, once again. If you haul large loads and use the gate a lot, the midgate enclosure wouldn't be a good option, and you may get sick of having to relocate an under-seat box for the conversion. If that's the case, a JL Stealthbox may be what you need, if you don't mind losing some center console storage space.
Tell us what you want and how you use your truck, and you'll get plenty of info in no time.