I wouldn't bother with the buffer. A naturally low PH can sometimes be better than adding powdered buffer.
not having any powerheads in the tank allowed the waste and food to accumilate onto the rock. Turning a high powered pump on could have stirred this up for your fish to ingest and if its riddled with bacteria and 'gone off' it would have a nasty effect on your fish.
Do you have a sump? you can put a filter sock on the overflow pipe to catch the debris. If i were you i would be carful obviously be use 1 over the power heads to blow all the debris off the sand and rocks to be collect in the filter sock. you'll need to leave the powerhead on for a couple of hours for best results but i would also be inclined to do a 20% water change just after you mix it up!
Obviously if you dont have a filter sock this cant be done!