Remember that the ignition is totally separate from the battery / lights etc so the engine will run regardless of battery state. Do you have a wiring diagram? According to mine, when the ignition switch is in the On position, wires red and black are connected, as are brown / white and brown.
As far as I can see the red wire is the positive feed from the battery, black is feed to ignition controlled stuff like the horn. Brown / white seeems to be input live for lights and brown output. I have a pdf copy of the manual with (almost illegible) wiring diagram if it helps.