Engine Noise coming thru speakers after hooking up amplifier?

I just finished hooking up my amplifier, capacitor and 2 speakers & tweeters and after I got everything hooked up there's now an ignition noise coming thru the speakers, the higher the amp is turned up the louder the noise becomes. Sound's great when the engine is off. When i disconnect the RCA cables... show more I just finished hooking up my amplifier, capacitor and 2 speakers & tweeters and after I got everything hooked up there's now an ignition noise coming thru the speakers, the higher the amp is turned up the louder the noise becomes. Sound's great when the engine is off.
When i disconnect the RCA cables there's no sound and when I connect the amp to my GPS's headphone port it sounds fine. I've connected the stereo in my car to an amp in my friend's car thru the same RCA cables and it sounds great. I've tried moving the RCA cables as far as I could away from the power leads as well as shortened the ground wire for the amp and still no help. All wires going into the stereo check out. Removing cap didnt help.
Stereo's a JVC KD-HDR1, amp's a Pyle PLAD618 2000 watt max 6 channel amp, 2 gauge wire for power and ground leads, 2.4 farad Voodoo cap, Voodoo spiral RCA cables, speakers are Fosgate 5 1/4 and tweeters are ran from amp in the stereo using the bi-amp mode in the crossovers.
Update: Tried changine ground wire on stereo to a part of the body, all of the low frequency noise is gone, bust there's still a high frequency noise while the engine is running. Would a RCA ground-loop isolater get rid of it? Or should I try upgrading to $30/pair RCA cables?
Update 2: I tried a ground loop isolator today and it didn't help one bit.
Update 3: I played with the ground wire to the amp and when it's not grounded right the noise is ALOT worse, so I don't believe it's that. I also tried swapping head units and no effect what-so-ever. But when I hooked up a friend of mine's amp to my system everything sounds fine! Bad amp?
Update 4: The noise does change with the RPM's of the engine. I imagine there's probably interferance coming in from my alternator or MSD ignition, but both are grounded properly.
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