When people talk of microbubbles and ready to quite, for contrast, I always think of a tank I cared for...it brought me to tears several times. (you can see the snail trails through the bubbles....and this was shortly after the window was "brushed" to remove the bubbles, done several times a day) Many things were killed (well, for this, and the copper) and it was always "cloudy" looking.
The ultimate problem on this tank was a fundamental design flaw. It was a combination of two large overflows that ultimately drained into one pipe causing a major cavitation, and zillions of microbubbles. When this water got to the sump, the water was moving so quickly that the tiny bubbles didn't have a chance to work out...and the cycle repeated. Lots of baffles were added to try and stop this, but I believe to this day it is still a problem.
But it can put things into perspective. Eventually I am sure that the source of your bubble problem can be identified. But it will take some time to try and come up with ideas, and talk you through trying things out.
Do you get any sort of "flushing" noise from your overflow and drain?