I would suggest that you be careful and not screw up your nice JL stuff before they even go in your car....
An alternator upgrade would be better than adding a 2nd battery. The 2nd battery will only help you if you plan on playing your system with the engine off for lond periods.
As for caps, JL does not make any. If you get a better alternator, you may not need any farad caps at all, but if you do want one (for show purposes), a 1 farad cap on the 500/1 will be fine. It's not necessary for the 300/4.
Lastly, $3000 for everything you listed above, including the deck seems like a lot. MSRP is my guess...
