Since you're keeping all of that my vote is new alternator and I guess you could do Big 3...it can't hurt.

This might help too. Ohm's Law Calculators This site maintains lots of information you might want to browse through as well.

If you do the math for all of your wires you can potentially increase the output from your subwoofers through efficiency. I think 4 guage is the minimum from battery positive but I think you're drawing too many amps for 4 guage.