6 with clunking when loaded

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2006 Whitewater pearl MazdaSpeed6 GT
A little background, I have been chasing this issue for about a year now...

I have narrowed it down to the following,
-1 clunk per rotation of tire/wheel.
-Dosent happen when driving solo unless I launch spirited ( I dont launch hard).
-Happens consistently when back seat is full of people or trunk loaded with gear.
-Sometimes it is a light sound only, but can be accompanied by a seat of the pants thud.
-Sometimes its from the right rear sometimes from the left rear.
-The lower the gear the louder the clunks.

So far I have replaced the propeller shaft(suspected CV and/or u-joints). Also pulled rear CV shafts and checked range of motion of inner and outer joints and felt for anything abnormal, nothing found (even took L/S to a re-builder and he saw no reason to open it up).
The diff is supported by the factory mounts, and the mounts and bolts are about as good as the factory can get...I know Im a tard for not switching yet, it will happen.

If you are still reading this you are somehow still interested so here goes the question...

Although my car is not lowered, the rear sits quite low. I think the springs have relaxed and are causing the CV shafts to bottom out to their minimum length. I would figure that anyone that has lowered their car would have experienced this? I am considering replacing the springs (with OEM) to see if the problem disappears. Am I chasing fireflies in the dark? On???

I am going to change the PTO and diff fluids this weekend, they are due and I also would like to not see metal filings or anything pointing at rear gear issues.

Help a brother - because I love my car and would like to sort this out before she goes into storage for winter.
 
Been under there a lot, all the suspension is tight. The clunking happens when the suspension is loaded such as launching or back seat full of people and the wheels rotating, nothing on a jump test (tried that). I measured the center of the hub to the fender roll, I have 14.5" at the front (fronts are new springs) and 13.25"(L)-13.5"(R) at the rear on P215/50R17 wheels & tires (spares while I refinish my rims and add new tires for next year). I also did an 4 wheel alignment, so the wheels are turning true. I would assume that most lowering springs are stiffer than the OE ones and hopefully would not have this issue. When I did the alignment (Sept 19th) I did happen to notice the the bound stoppers look as if they have been bottoming out. More fuel to my conspiracy theory
 
I replaced the PTO & Diff lotions, while I was under the car I scrutinized everything suspension related. I happen to clear the dust off the springs and noticed they were painted metallic black...thinking that Mazda wouldnt paint springs metallic, I took a closer look. Well it turns out I have Eibachs in the rear, which are notorious for sagging and would already be lower than OEM. That combination has me really pushing in the direction of my OP. Also the rebound rubbers inside the springs appear masticated. I am going to toss in a set of OEMs and see if my issue clears.

Now to find some time in my schedule.
 
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I have replaced the coils and have had a successful test drive with no clunking, and the car is driving smoother. I had a small vibration under hard acceleration that I only really realize now that its gone. Case closed, now I need to purchase a set of 33's to go with the 4x4 look!
 
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