the lights went out, are they supposed to? or is it a fuse?

there's also a 3 wire connector under the seat that can come undone.

Dave mentioned the clutch safety wire hanging out near the road grime and gunk.  I’d check the negative battery cable connection while I was looking around down there too.  Doesn’t sound major.  Just gotta find it.

Mine behaves exactly like that.  I have an intermittent clutch safety switch.  When the switch doesn't make good contact, it behaves exactly like yours.  Jumper the switch to test it.  Very easy to do since the connectors are readily accessible on the underside of the clutch lever perch.

Your headlight is behaving as expected.  There are two sets of contacts in your starter button.  When you press the button, one set of contacts opens to turn off the lights, while the other set of contacts closes to power up the starter circuit.  

Just unplug this connector and jumper the two wires.

just curious.  Does the tail light stay on when you press the starter?  
From what I can see in the wiring diagram, it should.  The starter switch kills the headlight, front running lights, and horn... but not the brake light, turn signal or tail light.

All of my bikes are stored indoors in a garage and my cafe racer is never ridden in the rain. Last August I washed the bike and took it out for a nice long ride with a friend. After a few hours we stopped for coffee and when I got back to the bike the battery appeared dead - like zero volts dead. I had my friend give me a push and the bike started right up with a classic push/jump start. I got home and again the bike wouldn't start. I assumed it was the starter solenoid acting up and parked the bike until I had an opening on my stand to address the issue.

Two weeks ago I got the bike on the stand. With a fully charged battery and the ignition key in the on position nothing worked...except the tail light. My first thought was corrosion in the ignition switch. I removed, disassembled and cleaned the switch contacts. Sure enough there was corrosion (the bike lived 100 yards from the ocean before I bought it) on the contacts, but upon reassembly the bike displayed the same issue.

I began the process of checking connections and noticed the headlight flickering when parts of the harness were moved. I could get the headlight to remain on, but as soon as I engaged the starter the electronics would once again die and I'd have to start moving the wires to the "sweet spot" to make a connection. I narrowed down the offending wire to the main ground that runs from the battery to the frame. I checked the battery side and all was good. I then checked the frame side and the cable looked good. Touching the wire to the engine it immediately made contact. To confirm this I removed an engine cover bolt and secured the wire lug directly to the engine case - and the bike started right up. I checked continuity of the wire while moving it around to see if there was a break in the wire below the insulation. Seemed good. I decided to just put it all together and that's when I saw the actual problem - the bolt that secured the cable to the frame had a bit of corrosion on the threads that made contact with the wire lug. When I moved the harness around it allowed some movement at the lug that made a slight contact - enough to make the light...er...light, but not enough contact to allow for starting current.

I cleaned the bolt and frame with contact cleaner and a wire brush and put it all together - problem solved. The moral of the long story is: the slightest bit of corrosion in the right (or wrong) place will shut down your bike. Had I not washed the bike the day of this ride, this problem may have never shown...until it was washed at a later date. That little bit of water was just what it needed to create the perfect conditions to become a problem. The problem itself was inevitable.

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