Bad welds and body flex? Is your dealer on crack? If they told you that then they're asking for it. If that's the case, they HAVE to fix the weld problem. It appears to me that they have no idea what they are talking about. The new chasis is quite rigid!
IMHO, I think it is something loose in the trunk. I hear a thumping noise whenever I go over a sizeable bump. Personally, I think it is the spare wheel cover with the tools attached making the noises. There's nothing else moving around in my trunk and it's clutter free.
The creaks probably come from the sunroof is you have one. They are supposed to have a fix for it. The rotten egg smell is probably just bad gas. It should pass...if not, get your cat checked. If the car does not track straight, tell your dealer to align your car properly.
Good luck!
