Reducing the fuel would be one way to get rid of the black diesel exhaust smoke, but it will reduce the max available power and the torque of the engine. The other two ways of getting rid of the smoke are getting more air, and increasing the combustion efficiency so the air getting through the engine is better utilized.
A totally stock setup shouldn't smoke very much however. If you've not already increased the fueling, there must be some other underlying problem causing the reduced airflow and/or reduced combustion efficiency that you should try to find and fix. If this is the case, consider performing the following checks and maintenance items: change your air filter, check your boost pressure and proper function of EGR system (if equipped), have your injectors spray pattern checked for proper finely atomized spray, check the tension of your timing belt, and the timing of your camshaft and injection pump. Look for any parts like camshaft lobes that are excessively worn or broken, etc. This can sometimes be a difficult problem to solve. Good luck.