With a cafe, anything could be different from stock. However, stock 550's all have a headlight interrupter when the starter button is pushed. If the switch in the control pod has *ever* seen brake fluid, it's plastic housing deteriorates, and the electrical contacts inside loose their orientation. Vibration can make them intermittent.
Or, the connections inside the headlight bucket may have become loose.
If it began life as an F model, another place to look for loose connections is on the frame, left side, under the tank.
You can get a multimeter for around 10-20 bucks. So, there is little excuse not to have one for probing electrical issues. Without it, you're pretty much in the take-everything-apart-and-put-it-back-together-to-see-if-it-works mode.
Cheers,