Maybe I can help since we are basically running ours the same.I too had bad micro-bubbles when I first set it up.
The return pump is split into two returns and one going to the fuge,right?I couldn't run the main valve wide open otherwise it was spewing microbubbles.The overflows couldn't handle it wide open either,it was burping badly.Mine is ran half open and I have a valve also to control how much flow the goes to the fuge.Maybe slowing the return will help.I still got microbubbles a bit but after a week,.it stopped completely.Possibly,the oils from the new equipment causing the bubbles.The coating of slime later on in the tubing and barb fittings,sort of a break in period for the new equipment helped stop them later maybe.