for big 3 wiring you'll want about 10 feet(estimate you might be better off just taking a tape measurer to your current wires) of
http://www.knukonceptz.com/productDetail.cfm?prodID=KCA0BK if you don't want to spend a bunch on it.
if you feel like going with full copper not CCA wire you should go with
http://www.knukonceptz.com/productDetail.cfm?prodID=KFX0BKyou can choose any colors you want just make sure its the 1/0 gauge wiring.
as for the alternator there are a few good choices but which brand you ultimately go with is going to depend on your budget.
http://www.soundqubed.com/AQ2200D-Amplifier_p_31.html would be the amp if i was buying a 2000rms watt sub.
are you wanting to remote mount your battery? because keeping it under the hood you'll need to measure the clearance because its easy to buy battery thats too tall when you order online.
also keep in mind the alternator upgrade is the only thing thats going to solve your electrical problems. alternator+big 3 upgrade are the first things that should be purchased and installed. after that i'd grab that AQ amp because its on sale lol.
as for your subwoofer choice i'd go with an FI btl n2 if i was shopping in that price range.
http://store.ficaraudio.com/n215/