A cap is like running NOS through your motor (or electrical system) whereas upgraded battery and alternator is more like rebuilding the motor to be bigger and stronger, then adding a supercharger on top of it. The cap may give a short burst of power like NOS, but in the long run, it isn't gonna help anything. Whereas with the upgraded alt. and battery, you have a constant supply of energy. A quick burst of power may be beneficial when racing the 1/4 mile, but not necessarily when jamming your subs for extended periods of time.
To the original post, another benefit of running 4 ohm over 1 ohm is sound quality. While it may not be easy to tell the difference in your subwoofers, when you get into your mids and highs, it makes a big difference. Most home audio and even some super high end car audio speakers are 8 ohm as opposed to the typical 4 ohm. If that amp really pushes the 1000 watts like alpine says at 4 ohm, then I would leave it at 4 ohm and not worry about the electrical upgrades other than upgrading your grounds. Do a yahoo search on "The Big 3" and you'll see what needs upgraded in your electrical system.