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It could be just about anything.
Rough idle could be vacuum leak, fuel, electrical, emissions controls, you name it. When the idle goes very low the alternator isn't charging as much and you see the lights dim.
Yes, the battery could be failing. Particularly if it is the original battery, you would be on borrowed time.
There were complaints of the transmission clunking when the vehicle was new, various X3 models. Not sure if there ever was a software update or not.
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2007 X3 3.0si, 6 MT, Premium, White
Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue
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