It looks to me like the return pump section is too small. You want the return pump section big enough to handle all the drain down water that occurs when you turn your return pump off. So if you set the running return pump water level at 2" above the top of the return pump you would probably need room for at least 3 more gallons of water which would drain down into your sump when you turn off the return pump or lose power. I would set the baffle in the first section (skimmer) at 10" and put your skimmer up on a platform, the baffle after your bubble trap would then be at 9.5" and the baffle at the other end of the refugium would also be at 9.5". I don't see a need for the last bubble trap. Unfortunately you will still likely need to increase the width of your return section even with the increased height.