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The 2 pin is for an LED that will blink out diagnostic codes (on my '98 V11EV"). Probably the same on your bike.
Ya, my 02 has that same small wire. I had no idea either. I didnt think the newer small ECM used a led code flash light.. but maybe its just a leftover from past models.
What? Guzzi would do that, and no documentation to boot? Shirley, you jest.
http://www.thisoldtractor.com/guzzi007/schematics/1998_EV.gif46 Diagnostic Connector47 LED Light