This article covers nitrate in detail:
http://www.advancedaquarist.com/issu...t2003/chem.htm
How much Chaetomorpha is being harvested out of the refugium, and how often? How much and what is being fed? Just the Cyclop-Eeze?
Those pumps should give more than enough flow for the system.
What animals are in the tank? What is the units on the alkalinity? 4.9 dKH is too low; 4.9 meq/L is too high.