The clunk issue is due to transfer case actuator gear. Just changed mine and the issue is GONE


Sent from my iPad using Tapatalk

Great info LeiZ. Did you do it yourself, or take it to a shop? How bad was the cost?

Thanks

Update:

Long story short... The reason my X3 was running rough was because the CCV valve had failed just like JCL predicted. Because the CCV failed it cause the motor to run rough at low RPMs, which caused the alternator to not make enough electricity which in turn made the electronics of the X3 work inconsistently.
Fixing the CCV made the transmission clunk go away when coming to a stop! I'm thrilled I don't have multiple problems... Just one problem with multiple symptoms.

So for the people in the future that search this topic, confirm that your emissions are in check and motor is running smooth before you go taking anything apart.

Hope this helps someone.