@DRNAB Yes - it seems that Mercedes are happy to fix it. One has to relax with these things where possible and have a kind of "knowing" that it will be sorted. To be fair to Mercedes they are quite good at getting something fixed and not arguing about in or out of warranty.
My advice might be to exercise your gentle rights and rather than piss about just ask them please to do the most they can do and then forget about it.
As for the wheels this is a tricky one. And might have been caused by the 11 year old not knowing how to drive a car with big wheels - again i think they are fair on that so long term its frustrating but they wil fix it.
Anyway we digress OP - HIJAAAAAAACKKKKK... ( only joking )
I have spoken to Huet's Car Audio today who calmly put my mind at rest that they will without question irrevocably find a way to remove this clunk noise. They are like the holy grail of show car sound upgrades.
It has emerged through research that JL amps are not necessarily recommended as the best option for OEM integration, which concerns me after I championed them here ( apologies ). The sound is good sure, but after 2 days in your silent barge of clunk on and off, it's enough to make you loose the plot and the will to live. Not Huet's fault.
The plan now is to look at JL directly and ask them why they do not have a time delay mechanism on their amps, and what makes them non compatible, and if they have comment on how to solve this matter without choosing another option.
Audison and Alpine both have time delay non clunk pop bang options - Yet Huets explained that the integrity of the sound is now a concern, by changing the amp the sound quality might not be as desirable. In their defense they were trying to get me the most sound possible and were not aware of how acute and irritating a mild clunk would be. And it is mild.
So far I would not recommend a JL amp until this thread has been modified unless there are options you have to remove noises.
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I am currently waiting on some more technical tips from you which I can propose to them, even though they are the UK market leaders, there might be something they can still learn from anoraks.
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A good learning curve for the E Class W212 sound system upgrade which hopefully will cure a lot of people's concerns - I will post more when I have more Intel. Additionally I will post the options open to you should you wish to fit a sub to an E Class post 2009
They are lovely people if you want to ring them for tech info 01273 441845