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.

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Pro motocrosser since 2005. First time BMW owner.
2002 4.4 E53