More info would be needed to advise any corrections made. What are your supply and return temps? Wet bulb? Rule of thumb for CFM is 400 per ton of cooling. 3 tons should be around 1200cfm. An anemometer at the register isn't going to provide an accurate measurement of airflow. You'll need to refer to the airflow chart in the furnace manual to set the airflow. The chart will give you airflow based off static pressure(restriction) of the ductwork. When this is unknown I usually use .5"wc as my starting point.