It's been a little over 3 years since I did it, but as I remember, the skimmer came with an adjustment on the body of the skimmer. I tightened down the blue adjustment knob so it was closed and attached a new air line from the pump and ran it to the outside and put a adjustable air line valve on that instead. If I remember right, I found a link to someone else who had done something similar to allow for easier and more accurate adjustment with the external valve. Also, the end of the air line can be aimed down and away from you so it's nice and quiet.
I do not remember having a problem with micro bubbles. I wonder if the skimmer just needs to break in or if there is some other issue. I do get a few bubbles in my display. You might be able to put a small mesh or sponge/filter somewhere in the chambers between the skimmer and the return pumps but that seems like it could be a pain and might create a breeding ground for some bad stuff. Not sure, just thinking "out loud".
I wish I remembered a bit more detail on this to help you but I hope this helped a bit. Good luck and have fun!