Yeah I think to better solve this problem, we need to know what amp you are running...subs could be rating 2000W RMS each, but if your amp is only 500W RMS. Then thats all you are pushing....
Can you tell us the amp you are using? Cause I highly doubt you are pushing 1200W to each, maybe total, but then still a 1.2 farad cap would suffice, putting a 5 farad cap on a 1200W system is just a waste. Also, do you have any other amps or other electrical devices hooked up? Sounds mostly like a grounding issue, and do the big 3 upgrade. If those two don't help, a bigger battery in conjuction with those two should solve the problem. No need for a bigger alt or second battery with only 1200W. Also, I would try to get my money back for the cap, and get an optima.
I'm pushing about 800W RMS total through my system on the stock 6i (90AMP) alt and stock battery. No cap. I did do the Big 3 upgrade, which is very helpful, very cheap, just takes a little time and effort.