the big 3 is actually quite simple as you do not replace the old wires , you simply add larger wires . the ground for the car flows the path of least resistance .
some things to check would also be adding a larger power wire from the alt to the battery, check battery and alternator state of health .
If your looking for a good read (very technical) http://www.newtiburon.com/forums/showthread.php?t=144225
... It has quite a bit of hardcore information .
I hope you dont think Im trying to bash/flame you , I am just trying to provide a valid argument for my view on the subject .
Edit : also what kind of amplifier are you using and at what Ohm load?