A capacitor is simply a big battery. It'll hold the power until it's needed by the subs.
I have no idea where you would get a bigger alternator.
I have 2 12's under my BubbleTop, and it's LOUD!! Better than loud, though, it's clear! The sound from these are amazing. I do, however, have all top-end equipment, including Kenwood Excelon head unit and amps.
I'll try to shoot some pictures tomorrow.
By the way - If you're looking for a BubbleTop to put over those subs, there is one on eBay right now- auction #230335524946
--Russ