alternator feedback

i have a 1993 mitsubishi eclipse, with a 3 amp, 10 speaker system.  a fosgate amp powering 2 12" alpine type R subs, an audiobahn powering 4 front speakers, and a small alpine amp powering two 6 x 9's.  2 speakers are run by a pioneer deck.  I removed the amp and subs to do some interior work, 2 months later i reinstalled everything and now i get bad rpm whine and low popping when the car isn't running.  I have a 1 farad capacitor and an extra battery in the back.  2 preamp outputs from the deck control all 3 amps.  i've created a common ground with all amps and deck, changed rca cables and preouts, cleaned all terminals, and isolated each amp, and speaker and with little to no effect.  every speaker will get this noise from any of my amps using either cable and preouts i have.  What else could i possibly check?

all i need now is confirmation.  I kept playing with it and found that grounding the rca cable is the only thing that improved it, but not 100%. then i hooked up my ipaq computer directly to the amp and viola! perfection!  So, can i assume my preouts are fried???