That should be sufficient flow!
Not sure I necessarily agree. With an almost 50% addition in live rock, there was undoubtedly an increase in "dead spots" with respect to flow. These dead spots are probably accumulating detritus from those large detritus-producers mentioned earlier. I don't mean to discount the effects of dyoff from the new rock, but the decomposing detritus is probably contributing organics that are feeding the HA.
(was the tank always low pH, or just recently? the reason I ask is that organic acids, which would lower pH, are intermediate steps in the oxidation of organic waste)
Also a couple of questions about the sandbed removal. First - how deep was the sandbed initially?
And Second - did you remove half from one end of the tank (no change in depth of sandbed in the other half of the tank), or did you take out the top half all over?