wow. If you're having power issues running a 200W sub and a 4x45... I'm in trouble. I'm going to be running a 500/1 and a 300/2 JL Audio.... 800 Watts total, and I was planning on going the Vishnu path myself next Spring. I may have to end up tossing another battery in the trunk.... blech.
Yeah, i'd go with what Tony suggested. Take the Cap out of the equation first and see if that helps.
I really wonder what is causing your power issues though... that's the odd one. Where did you ground out to? I'm going to upgrade grounds from the battery to the alternator and the chasis eventually so everything has the same potential through 4 gauge.