The lights and regulator are in a different circuit than the ignition, the only common path is the ground.
There are differences in the ignition system on different year sleds. I assume your sled is a 1998 or earlier. On the early Phazers there is a black and white wire from the CDI box, on later models it was yellow and black, I do not know what year it changed. Unplug that wire and check for spark. If it has spark, the ign. switch, kill switch or TORS switch is at fault. The TORS switch is located on the carb assembly. To check it, unplug the switch and plug the wires from the harness together and check for spark.
Try that first.
If you have an owners manual, there is a wiring diagram in the back.
It would be good for you to have a service manual from Yamaha.