Ok so you have a bad wiring harness on the engine right? As for the idle problem I would suspect a bad Electronic accelerator, Idle speed control and cruise control unit . which is the throttle valve .
All of these controls are built into the throttle assy. The harness on the throttle valve do cause problems ( I have about 10 on display in the shop ) . What I would first do is have the codes pulled from the diagnostic module and the ea,isc,cc module also. As for the noise in the rear end well if the vacuum and control pressure is off for the transmission it will cause a clunk on downshift, also a bad flex disc or worn rear differential bushingswill cause noise also. I have seen alot of things cause noises in rear ends when coming to a stop. Basically you need to find a dependable shop who has a good reputation and experience on Mercedes. Good luck,