Golf VI R :: Drivetrain Clunk / Pop When Engaging Gear And Shifting 1st - 2nd

I have been reluctant to post another clunking thread because it's nearly impossible to accurately describe what is happening. But I have reached by breaking point and I wanted a few opinions before I take it into the dealer. I am still under powertrain warranty, but I want to be confident I am not wasting mine and the dealers time if I am just missing something easy. I also know dealers don't always take clunks seriously so I want to pinpoint it first.

Symptoms : Car has 50k miles. I am the original owner.

From a stop, when getting the car rolling moderately aggressively there is a clunk/pop noise from the car. I can slightly feel it in the pedals and it is fairly loud. Almost like a distant hammer and nail pounding. It's a single clunk, with sometimes a double "pop pop". It's noticeable even with the radio turned up a little. If you are smooth on the throttle it doesn't make the noise. It seems random, like something is hitting something which only happens under certain weight shifts.

It sounds like it's from the rear and the front. It seems to switch. But honestly I am not confident either way. Where it is. It is silent on turns, bumps, speed bumps, driveway, etc. I don't think it's the suspension. It is not a clicking/tapping, only a single clunk or knock.

It also happens in 1st/2nd in stop and go traffic. If you leave it in 1st and the traffic is moving from say 8-15mph where you don't need to use the clutch it will clunk during on/off throttle. Anything above ~30mph I haven't been able to replicate the noise with on/off throttle.

It also does it if I downshift when coming to a stop and don't rev match. Say you are slowing down and you go from 4th, 3rd, then 2nd, let the clutch out and it rev matches up to ~3,000rpm which causes the weight to shift forward....clunk! It is not easy to replicate which is another reason I am slow to bring it to the dealer until I pinpoint it.

Things I have tried:

- Subframe bolt torque check. Installed ECS spacer/bolt kit anyway.
- Sway bar links are tight, or at least they didn't budge at all.
- Adjusted the rear hatch a million different ways as it was making a similar noise earlier.
- Spare tire tightened, tools removed
- Rear seats up/down/mix/seat belts fastened, etc.

I was only able to locate one motor mount? Where they are. Seems fine. Dogbone seems fine, again hard to tell.

Suspect:

I have VWR springs, but I am 90% sure this started happening right before I had them installed. I did the rears myself, a well known shop did the front. I noticed the noise maybe 2k before the springs were installed.

Clutch linkage somewhere - I had issues with my transmission (early build). The clutch was replaced at 7k. I've always had a very loud flywheel and a grinding feeling in the pedal. Maybe the shifter linkage is hitting something? I have little experience with VW's so I am still learning and don't know what to check.

My rear harmonic balancer is cracking like everyone else. I have no vibrations yet and I don't see how it could be causing a clunk in the current state. Maybe a motor mount is bad that I cant see? It feels like something is loose in the drivetrain.