Tuning the PID with the motor running forward was easy but transition to backwards was a completely whole new pain in the ass. It works now both directions flawlessly, however there is still a bit of overshoot only when moving backwards starting at 0 RPM because it runs forward a little bit and then in the right direction while the system compensates the error. 

In the next entry I will explain how I fix the issue and also how to do the PID control like a pro using only simple and standard equations ;)