I agree, I would definitely run your doors off an amp if you're planning on a ~4kw sub stage. Plus if you look around you'll see that you can get good 2/4ch amps for a fair price.
Don't forget to take into account what you're doing with your door speakers when concidering a head unit and amp, as their are many options available. Are you going 2-way comp, 3-way comp, individual pro audio speakers, do you want to run active or passive, do you want to use your amp/a processor/or the head unit to control your equalization/sound stage?
"Vitto" hit it on the head on the importance of proper sound deadening!
If you don't know everything you need for doing the Big3 I'd suggest checking out http://www.ceautoelectricsupply.com/. They have complete kits and from my research, great customer service.
I personally will be running Skyhigh wire. It's great wire, tru AWG, AWESOME customer service and a fantastic price point. I see a lot of builds on here with RF, Knu, Audio Technix and welding lead also. Any of these should serve you very well. Another thing to think about to save a little cash on your wiring is the use of CCA where you can. I am personally doubling up my front/back runs using (2 runs pos and neg) of 1/0 CCA, and using 1/0 OFC for my Big3 and all rear power runs to amps. I can do my CCA runs for 1/2 the price of OFC front to rear, and I still have a combined 500amp wire rating to feed my rear batt bank and amps. Just food for thought.
As for your box, during your design stage please dont forget about how your going to properly secure the enclosure to your vehicle! Also, Torres was mentioned already for actual dimensional design and tuning. If you don't have it already, also look into Sketchup. Its a great program to model and fine tune your box in 3D. Lets you see exactly what the finished product will be before building so you can make changes if need be without wasting money on ruined materials. Also, it seems obvious but decide how you're going to wire your subs... bolts through box, terminal cups, wires from subs just ran through a hole in the side of the box then sealed?
Just remember to think, research, plan...and then do it all over again lol, and you should be good.