2004 had the GM 5L40E according to my source, same as the X5 six cylinder. 2007 models went to the ZF 6 speed I believe, but a smaller ZF than the one used in the X5 8 cylinder models.

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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