YouE planetary motor is having problems how do I pinpoiont the problem?
The specs reads: max. 36 volts 
I switched over from SLA 36 volts to li-ion 42 volts. 
Some assured that it's within tolerance but I suspect that these Chinese controllers are also on the cheap side and aren't as robust to take on that much more above tolerance continuously. 

I got my new controller and now everything is back to the way it was. 
I got this controller:
http://www.ebay.ca/itm/36V-48V-350W-Electric-Bicycle-E-bike-Scooter-Brushless-DC-Motor-Controller-/172878396579?roken=cUgayN&amp;soutkn=IvO9vJ

I tested the throttle to make sure that it was giving the proper ohms. Check
I tested the magnets by short circuiting the 3 phase power for the motor a felt a turning resistance. Check
I bypassed the ignition and the brake switches, connected the throttle, then the 3 phase wires and connected the controller's self-learning wires and then the power. 

Before I was able to connect the hall sensors the motor was turning at about 1/4 power and I discovered that in learning mode it learns to know what direction to turn the wheel and gauges the throttle resistance. 

When the controller is powered and you disconnect then reconnect the learning mode wires while the motor is turning the motor will turn in the opposite direction. Also, in learning mode, if you turn the throttle the controller will learn to add more speed based on the change of resistance of the throttle. I went full throttle and it slowed the motor but another twist and it accelerated the motor. It figured out how it should react to it.

I hope this can be useful for those who need to figure out replacing a new controller.