I believe there are probably two factors which over time might have a cumulative effect of dropping your pH.
1) In a single chamber model your probably dosing you tank w/ trace amount of CO2 which will lower your pH
2) Your adding lower pH water (the efluent) directly to your tank
My reactor...
It is my understanding that comming out of the first chamber (in a dual chamber or only chamber in a single) if the pH is below 6.5 it will eventually turn your media to mush and any thing over 7.0 and your not disolving anything.
I keep my at around 6.6 - 6.7 so there is a small cushion on...
Even if the bottom is tempered the sides should not be. I would partition off the wall side of tank (making one large overflow) and then you could drill the sides for one or two 1 1/2" bulkheads.
Did this make any sense?