I guess it depends on how in-depth you want to get into it. Since there's an infinite number of ways to modify the NES, heheh.
If you just want to swap out the red power LED for another color, that's pretty easy. Or you could overclock the CPU, heheh.
http://home.arcor.de/hipohipo/nesoverclck/Overclocking%20the%20NES%20by%20WhiteDRG.pdf
On the other end of the spectrum, you could remove the main chips from the system and design your own computer around it.
Mostly what you need to know is that it's all digital. "ones / zeros", "on / off", "5V / 0V", "high / low", "VDD / VSS", all means the same thing. If you want to get straight to the useful stuff, learn how to use digital logic.
http://www.play-hookey.com/digital/