And of those, the E83 LCI (2007 onwards) had the higher horsepower N52 engine and still had the manual.

Apart from the E53 and E83, there are lots of BMW sedans with X drive and manual transmissions.

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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