Pretty simple to log onto www.bmwusa.com, select certified pre-owned (CPO), and do a dealer search. I looked today and there were 138 manual transmission X5s listed. Not much there at the moment for 2006 models (just one), but there are 133 of the 2007 models listed. Take your pick of colours, options, and locations.

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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