I'd completely forget about the stock amp and the Pioneer's internal amp (except maybe for the rear door speakers which I'd leave stock).
If sweet sounds are what you crave, you need a component speaker set up front driven by their own external amplifier.
As for capacitors, you'd be better off investing in a higher amperage alternator, IMHO. But, I'd hold off until you notice an actual drain when the system is on, such as the headlights dimming to the beat of the music. Otherwise, you'd just be wasting your $$$$$.