Why dont we stop dissing caps? Everyone who actually cares about their build knows they are garbage, and all the ricers think they are hot stuff. Get a second battery if need be, but never get a cap. Also, unless you are burping the subs constantly, I dont think you will need a new alternator, although I am sure it would relieve some stress off alt if you got a better one, but no need for a 300Amp alt when only doing like 1kW.
I have been holding off, but I need a new alternator for my sound system when I install it. I have this choice right now - Either have 3 seats in the back, or have 1 amplifier thats the size of 3 seats...decisions decisions...
P.S. If I was in your shoes, I would run to the local auto store or where ever you can get a small sealed battery and buy it. You dont need some batcap xtreme or anything, just a small regular car battery will work fine. Put it in with your system, because everytime that your lights are dimming, it means you electrical system is working hard. I would personally wire the second battery up with a solenoid that lets it charge when the ignition is on, but it will not drain the other battery when you are not in the truck. This would make the subs on a somewhat separate electrical system, so they don't strain your vehicle.
Sorry if that was too much text