Given that idle while stationary is fine, but it is not fine when moving, I would be looking to the transmission more than the engine electronics. There is a harness to the electronic transmission control (which communicates with the engine) and it is far more likely to get water into it than something on top of the engine like a sparkplug.

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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