The main fuse should be ok. If it was blown then you would not be able to start the scooter.

So sitting on the stand and revving the engine does not cause the fluctuation in the lights?

Motion is affecting the circuit because you said on acceleration the lights change intensity.

Is the taillight (not brake light ) off when the headlight is off?

Seems like you are getting a back circuit to your lights through the brake light switch. So something in the headlight/tail light in not supplying power.

Does your owner's manual have a wiring diagram?