that whine is not your alternator going crazy.
what it is is the RCA cables picking up interference from the power cables. or possibly ground loop interference.
1) did you run power cables up one side of the car and RCA (signal) cables up the other?
2) where did you mount the ground for the amp?
if the rca cables are close to the power cables, then they will pick up the magnetic field that is around the power cable, causing a whine noise from the sub/speakers. so keep them apart.
if you have already kept them apart, then u can try grounding the headunit where you have grounded the amps. stopping ground loop interference.
i would suggest upgrading the cable that runs from the chassis to the batters )negative and from the block to the negative terminal of the battery to around 4AWG cable. make sure you have grounded the amp properly too.
maybe the settings on your headunit are wrong, spl bass is normally around 45hz, and there should be plenty of functions on your H/U to bring out the full potential of your system.
with the battery, if your serious about getting one, go and get a dry cell excide or optima, forget about caps as these batteries have an extremely low ESR anyways. (the speed at which the battery can release power)
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