Please Help, 2 different noise problems in system,

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I need help! I have invested alot of money and even more time setting up my truck's audio system and now I have 2 noise problems.

First here's my setup if it will help:
1- Power Acoustik Goth Series 820 amp bridged @460 RMS
to a JVC 10" sub with a double stacked 86 ounce magnet and an aluminum cone. (Similar to the Alpine E series subs, but has a bigger magnet.) in a custom Bassworx ported enclosure.
1- Dual Amp, bridged power- 280 watts RMS connected to a new Sony 12" sub in a sealed box.
2- Kicker KS60 6.5" speakers on a custom-made panel I made to fit my 1995 Nissan EXT CAB 4x4's back cab wall. These speakers are only getting 22 watts RMS each from my Pioneer SuperTuner3 CD head unit, but they sound great. I put bass blockers on both of these. I also have about $250.00 worth of Accumat in my doors, my back cab wall, and all my speaker baffles. I also have about a 1/4" layer of bedliner spray put on the inside of the roof of my truck, not to mention about 5 cans of GREAT STUFF foam spray at various locations.

In my door panels I have a set of Pioneer REVS 6.5" with the Kevlar cones. I had to do some significant work on the inside of my doors for these babys to fit. They are being powered by a Dual amp pushing them @70 watts RMS each. These are the baddest coax speakers I have ever heard.
I have a 4 guage power wire running to my Interstate Megatron battery, with a 100 amp fuse block @ the battery. This power wire runs to the back of my cab, where I have another Tsunami 60 amp block. Then I have a Raptor 1 Farad capacitor with a 4 guage ground. From there the power enters a Tsunami dist. block where the wire size drops to 8 guage for each of my 3 amps. My RCA cables are seperated from my power. My head unit has 2 sets of preouts so I used the rears for my 2 amps and 2 subs. My Power Acoustik has a set of RCA outs. I have the amp powering my Pioneer REVS connected to the head units front RCAs. My farad meter is showing anywhere from 14.4 to sometimes as low as 12.5 when I crank it up and my subs put out some notes that actually blurr my vision.

I have tried running my amp remote wires 3 different ways and I still get the same results. I have ran them seperate, together and finally I just installed a toggle switch with a blue LED light neatly under the right side of my steering column, but I still get a major turn-on thump.

When my amps power on, trucked cranked or not, the thump pushes the diaphrams out on all of my speakers hooked up to an amp. Also my door speakers, which are hooked up to my small amp have what seems to be alternator noise. However, this noise is just as bad with the engine not running as it is running . The only difference is I can hear the RPM whine while it is cranked. This noise is very noticable with the volume turned all the way down. I did have my amps grounded to seperate chassis points, but now I have the amps grounded to the same chassis point. Still no improvement. So next I installed a 10 guage chassis ground wire to my head unit, instead of the much smaller and longer ground of my harness. Still, no improvement. Tommorrow p.m. I plan to install a 3 way noise filter to my head unit but I really don't want to have to do that. I am very maticulous about doing stuff right and I have to much invested for this to be let go. The whole system sounds terrific and when I play it pretty loud it isn't noticable, but I want it to be right and not cause any damage to anything.'

Extra info: The capacitor is mounted about 14" from 2 of my amps. I have my 2 sub amps mounted vertical one above the other. Can someone please offer me some advice on how to solve this problem? I will go to any lengths to make it right.
 
I'm no ICE guru, so this is all guesswork and I could be way off the mark, but with that level of RMS output power I guess that there's a switched mode PSU in there somewhere to get the supply volts to the power amps up. SMPSs can generate a lot of low frequency audible junk especially at low load, mainly due to drive cycles being skipped to get the average power down below what the smallest duty cycle capability of the PWM chip can manage, but it can just be due to design flaws (e.g. unsuitable compensation, track layout).

So, if you have you access to the higher DC volts output going to the amps(s), you should be looking at a common mode choke in series with the DC output and possibly a dummy load across it to get the SMPS output load above the minimum level where cycle skipping may be a problem (perhaps a few hundred mA). It may be worth passing some of your thick cables through ferrite doughnuts as well. One trick for finding where noise is being injected or generated is to have a 2ft length of insulated wire connected to a needle probe, stab various cables with the needle while listening to the buzz and if it changes for better or worse then that where the problem is.
 
If you have both whine and a turn on pop when the head unit is plugged into any single amp, the head unit may well be damaged.

Pull the head unit and disconnect all RCAs. Set your multimeter to ohms and measure the resistance from the outer shield ground of the head unit's RCA outputs to the case of the head unit. The resistance should be very near zero ohms. If it's not, you very likely have burned the shield ground in the head unit.

As a temporary fix/test, you can connect a short piece of wire from the RCA shield to the case of the head unit. Do this while the system is powered down. If the whine goes away, the head unit is in need of repair. If the whine is gone but it still pops, you've blown the muting transistors. It will require an experienced tech to replace them.

Let us know what you find.
 
However, this noise is just as bad with the engine not running as it is running .

Ah,well that isn't alternator noise then.
Engine not running = alternator not spinning,there CAN'T be alternator noise. I'd check the fuel pump,they're common sources of noise. (and commonly turned on with the engine not running.)

Another thing i've had issues with is the dimmer for the dashboard lights. Try dimming them and seeing if the noise changes pitch.
 
Thanks guys

I'm going to try both ideas. I'm also thinking that one set of my preamp outs in my head unit might be bad. Even though I get the turn-on pop from all 3 amp setups, I only get the engine whine from the amp hooked up to my front preamps on my head unit. Yesterday I just turned the key on and turned my head unit on with the volume all the way down. An old man across the road was driving his tractor and I could hear it through my speakers. weird huh?
 
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