dang, that is too hot.
is your motor a true 540, or a finned out 390 size?
If its a finned out 390 then that makes some sense. A smaller motor makes less torque and needs to be geared down some.
The traxxas vxl motor is a 3500kv 540. It will run close to 200 on stock gearing/tires on a 3s lipo in the grass.
Note, grass driving provide more drag then on pavement. Even with a vxl powered stampede, 3s should really only be for pavement and not offroading.
However, you can just gear down your current motor (whether its a 540 or 390) to lower the temps.
Id suggest going to a 90t spur and 15-16t pinion. This will reduce top speed, but make it easier for your motor to get upto speed. This reduced strain will lower temps.
Adding a heat sink with fan wont hurt either. But you want to get the motor into the 160-170 max range for it to last a long time.