Increasing the flow rate might allow you to add more carbon dioxide to the reactor, and thus possibly increase the dissolution rate. I am not an expert on calcium reactors, though. If the pH of the effluent is still very low, then a second chamber of media might be appropriate.
I agree that checking the dKH of the effluent might be useful. You can dilute it by a factor of 4 (three parts tank water to 1 part effluent) and measure. That might be easier than titrating full-strength effluent, although both approaches might work.