Turtle when you say you are struggling what is the car doing wrong?
Also you will find the 540 motor does get hot in the car. I reckon this is due to the fact that the bottom vent gets covered by the chassis but with another person i know racing the cyclone S they seem to think its fine with the motor.
I dont know about gearing but with 540 i used to start with a rollout around 38-44mm. Probably best to start around 38mm.