So I got back from my business trip and hit the library. I didn't have a card, but within a few minutes, I did and was out the door with the book... All 350+ pages of electrical glory. I went through the whole book and wrote some notes down. It looks like the only thing that I missed was the previously mentioned junction box issue. I have everything else. The wires themselves are run correctly, stapled down correctly (ok, maybe a little overkill on some of the staples), I had enough length of wire coming out of the front of the box (I targeted 8 inches, and code requires 6). So after spending some time with the book, I headed downstairs tonight and started ripping out all of the old wiring that was going from the breaker box to the junction boxes. What a pain, but it is done and ready for new wiring to be run tomorrow. I might as well hit the home improvement store and pick up another 250 foot spool of 12-2 wire (20 amp circuits) for $76 plus tax.

I wonder if there is any way to recycle the old wire's copper? I mean, some people steal this stuff from houses that are under construction, an honest guy should be able to get a few bucks too I would think.

I will wait until I have to pull out the wiring for the existing lighting as well so that I have it all out at once, but I can't do that until I am ready for inspection.
2-M60s, VP180, 8-M3s, SVS 20-39PCi, DIY Sub, 8-Shakers, JVC RS45, Anthem MRX-1120