OK, as far as speaker wire goes, I run 14 Gauge wire to all of my speakers in the car... I run 8 gauge from my amplifier to the subwoofer. A good rule of thumb is to just go overkill. But to be honest, 16Gauge is just fine, especially for what you are running...
factory wiring is usually reallu crappy 22gauge wire... I would NEVER run aftermarket speakers through factory wiring... why limit yourself?
Also, from my experience, if you have decent gauge wiring, then the insulation is usually good enough so that you can run it next to your power wire going to you amplifier... what can make a big difference (from my experience) is the RCA cables. Some RCA's are VERY sensitive to power/ground wires next to them. I run these
http://cgi.ebay.com/ROCKFORD-F...0.m14 , they are directional, twisted , MATRIX Rockford Fosgate signal cables going to th amp, and 14 gauge wires going back to the speakers. So its a good idea to run the RCA's on the opposite side of your power wire... but for the speaker wire, I run them up the side that they are going on (left speaker up the driver's side, right speaker wires up the passenger side, etc.
Going to the doors, you simply remove the door shell, then you can use a thick long zip tie to get the wires up through the hole in the car trhough the black rubber thingie into the door... these directions should help on removing the door...forums.altimas.org/zerothread?id=330757
and to get wires into the door, follow these directions on my kickplate installation thread
http://forums.altimas.org/zerothread?id=348881