The "Starter Disconnect Switch" is your clutch switch and needs to be closed (short together until you get connectors on them to hook to the clutch switch). The Start/Stop switch (red three-position switch on top of the right handlebar control) needs to be ON (center position) for the ignition to fire. The starter will crank, but the ignition won't fire. Also, either the bike needs to be in neutral or the neutral switch lead grounded (Neutral light on) to crank unless the clutch switch is made up. This is to keep you from starting in gear with the clutch out and the bike taking off - it happens!
BTW, I know of no transistors outside of the regulator and no relays outside of the aux lighting circuit on GL1000. And none of these really have anything to do with cranking or firing the plugs.