I don't mean to be a smart a** but is the "Sensor" you are referring to located right between the shock absorbers? If so, the "Sensor" you are looking at is probably the Drain Plug for the Transmission.
The only sensors/switches on the transmission are the 5th Gear Speed Sensor and the Neutral Indicator Lamp Switch. Since you say your 6th Gear Light and Neutral lamp are working, those items are OK.
Are you sure this wire is supposed to go to this Engine/Transmission? Maybe it's a wire from the bike, as someone else suggested, like the rear O2 Sensor, or the exhaust bypass valve that is used on European export bikes.