Simply over thought. A mongoose system is rated for 3s battery. The system will not draw more current then the Battery will allow ( 20C, 30C, 40C....) If you are running a 9000 system with a 3S Battery. I would check the gearing and find the Highest C rated Battery from a reputable manufacturer. Example below... Check the esc for current rating. I think the mongoose is 40 Amp per phase. So if you are running the 20C pack, you exceed the constant which will cause it to get warm.
- Typical measurement for 20C battery 18C continuous discharge rate of 36 amps with 50 amp bursts
Hope this helps.. Just read the spec sheets.