I doubt that your factory alt can even think of keeping up with the 1000. it will draw up to 75 amps itself. just getting a cap wont help if your alt cant recharge the battery and the cap. it wont matter if you have 2 batteries and a 20 farad cap. best bet is to upgrade your alt to at least a 150 amp or higher. dont forget about the grounds and power wire upgrade too.
It sounds like your draining the cap to fast either try a 10 or 20 farad capacitor or a second battery even both i have a 1000/1 and a 300/4 with two 1 farad caps and the amps still make my lights dim and feel the altenater working when the bass hits. also check the gound wire and make surethe wire is metal to wire for a good ground it should help good luck man!
If the amp was hot, it probably has a serious problem. You should have it checked out by a qualified tech. Don't continue to use it. More serious damage could occur.
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