I've got a 2009 2.8CRD
HAd water leaking in through the rear wheel arches into the back floor wells.
Have you checked them out. Carpets will carry water every where.
Dealer did 'water test' after taking all the carpets out.
Had to remove rear flares and seal up holes.
Been fine since.
Why there was holes there was never explained.

Let the dealer sort it out

 

pull out the carpet and bed line your jeep

 

mine is at the line-x dealer right now getting sprayed

 

pics or never happen!!

 

What was the issue with the door sill? I have the same issue and have not yet found the culprit.