I picked up a XB12R project and all of the wiring was unplugged, moved and otherwise molested. I have the bike completely sorted except this one plug, wire exits from the left side of the bike, 4 wire plug Red, Black, White and brown. See photos below.IMG_5951.jpgIMG_5952.jpgIMG_5955.jpg
That module should sit on top of the airbox that is missing from your pics, should have a cable running to it as well. If you have a CEL, it could be why. Get the codes with the data plug, (instructions in the manual link I gave you), or ECMDroid (Free on GooglePlay) using a Bluetooth dongle (I love my Buelltooth from Rev-mo.com) to your Android device.