Have already replaced the plugs with Denso Iridium plugs - the ones
spec’d by Toyota.  I’ll work on it some more this weekend and post
back with my results.  Thanks for all the suggestions

I doubt if replacing the coil packs will make the noise go away.

As someone asked before, does the noise come on both CD and radio?

Try unplugging one speaker at a time to see if one or more of the speaker
wires are picking up the noise.

Well, you've done your homework! I would still ground everything to the
same point.

Note that I wrote the rest of this and added this later...what are you
using for ignition parts? Genuine Toyota? You describe spark plug noise,
this can be caused by the plugs, wires or cap and rotor. Since Ray
mentioned something about coil packs, what are you using for plugs? I use
NGK R-Type (not "R" as in 'ricer'(sorry...) but "R" as in Resistor) If
you're using Split-Fire or any of those other supposed 'hot' plugs, trash
them and use NGK or Nippon-Denso.

OK, now onto the rest of my "Best Guesses"...

The only other thing I can think of, and I have never tried it because a
little noise doesn't bother me (and, I don't have the snapping sound
you're describing...now) is to try a cap on all the inputs. I think these
things are bling, too, but what you're describing is an AC type sound (as
opposed to DC) and the job of a cap is two-fold: it provides 'hold-up'
during large voltage spikes, but also, a cap with the + side tied to a DC
power source and the - side tied to ground passes AC 'noise' to ground (A
capacitor used as a filter passes AC and blocks DC). I don't know if this
will do it, and large caps are expensive, but for the amount of current
you'll be passing to ground you can use something like a 10 Microfarad. Or
get some of those toroidal choke coils at Radio Shack and wind the power
wires to it.

It also help to isolate where it's coming from. This is going to be a
pain! You'll have to connect the speakers to the head unit, bypassing the
amps and see if it goes away. Then add the amps back in and see if it
comes back. You said you put a filter on the head unit; try one on the
amps.

Also, check with a local stereo shop. They may have seen this in this car
before and have a quick solution for it.

I *HATE* this problem, since there are so many variables it's hard to
determine what will fix it. I would still start by running all the grounds
together, and then work from there.

At least when this guy posts, he makes it a toughy!!!   ;)

Again, if you resolve it, let us (or at least, me!) know! I've been doing
car stereo installations for about 25 years, and only had this problem
once...(and can't now remember the solution...)

I do not think it is the ignition coil because it would have caused the same
problem with the factory radio, which it apparently did not, and you did not
mention any kind of drivability problem.

This sounds kind of stupid, but try shielding the head unit and amplifiers
with foil and see if the sound changes at all.

Try shielding the wire bundles near the head unit in addition to shielding
the head unit.  Also make sure the power and speaker wires for the head unit
do not run near the ECU.  Instead of routing the right speaker wires near
the right kick panel, fish them down the center of the car and cross to the
side under the seats.

Holy crap! When you pose a problem, you sure make it a good one!!
Now when you say the noise is there with accessory on, is it also there
with IGN on, and/or the engine running?

And, what do you have for accessories that would be powered up with ACC
ON? Do you have phone chargers, XM or Sirius satellite receivers, GPS, etc?
A dealer installed alarm system? (I trust you see where I'm going here...)

I don't think it's anything TOYOTA installed on the car, more likely
something either the dealer or you added. It could be the dealer installed
something behind the dash that is interfereing with a more sensitive radio.

Also, is it there no matter what the input source, or does it go away when
accessing a CD or iPod, etc? Do you HAVE a direct iPod input? The JVCs
require a proprietary cable to add a line in, and these can cause problems
depending on what they're located next to.

Also, try turning on accessories one at a time; wipers, rear defrost,
heat/fan, etc and see if it gets worse. Then I think you'll find the
culprit.

Man, every once in a while someone pulls a real stumper out of the
air...you win the prize this time!!!   ;)

Good luck!

Oh...going over your original post, try swapping those Fosgate wires
with...Playstation wiring...it's well sheilded for being located close to
a large electro-magnet! ;) It doesn't have to be name brand; Wal*Marts
mid-priced set will work.

You say try "shielding" the wire bundles near the head unit.
Shielding them with what?  I’ve already tried wrapping tin foil around
them, but that made no difference.  I’m not sure where the ECU is?
But...there is a large metal "box" type of thing straight behind
where the head unit sits, which I think may be it?  But...the problem
is...there is no way to route the wires/cables away from it!  They
have to sit somewhere back there when you put the head unit back in
place, so....they’re always gonna be somewhat close to it - it’s
physically impossible for them not to be.  The speaker wires are not
routed through the kick panels and dont’ seem to be near any wiring.
They’re up through the top of the door panels and then come down
through the sail panels (I think that’s what they’re called?) and then
down into the front doors.  I’ve tried re-routing the signal cables
behind the head unit a million different ways - no difference

I agree with you about taking it to a car stereo installation shop;
however, unfortunately....money is the issue there.  I fear an
enormous charge and them ripping the entire system apart and starting
from scratch, etc.  Or......my other fear is they turn around and say
they don’t know what the problem is, charge me an arm and a leg...then
I’m still stuck and have to bring it to a garage to troubleshoot an
electrical system issue and.....you know how that goes!   Anyway....I
am about out of tricks though and I think I may stop by a shop and see
what they have to say.  Thank