The engine needs to be in neutral (or clutch in) to start with the side stand down , the neutral sensor is in the gearbox, clutch switch on the clutch..
To run in gear, the sidestand needs to be up (you have no sidestand, so no sidestand switch) therefore, the engine module thinks the sidestand isnt up . The green and the green white wire need to be connected to simulated stand up.
Try disconnecting the clutch bypass, this is only needed if starting in gear.