Bambam,
First thing you may want to do is contact Hobby Zone's technical support to see if they have any suggestions for the problem. They have some of the best support in the business and may be able to solve the problem.
If you want to upgrade the motor as others have done, you'll need to replace a number of items. The stock receiver and brushed speed control would be replaced with separate receiver and brushless speed control. The brushed motor would be replaced with a brushless motor. You'll need to buy or fabricate a new motor mount as well, plus figure out how you want to get all the new wires run.
None of that is incredibly hard, but if you haven't done it before it will certainly be a task, but also a good learning experience.
On a different note, be careful with how much tape (weight) you add to the rear of the plane. Pushing the Center of Gravity back is sure to make the plane fly poorly, or even un-flyable. The Super Cub is pretty forgiving, but every plane has it's limit.