from what i can make out of this design, you may have some major micro bubble issues with it. I am just guessing, but it looks like the refug over flows into the return chamber, if the water level in the return chamber fall below the 7 inches you will have some turbulence right in front off you return pump which is not a good thing. also the bubble trap after the skimmer is not needed from what i can tell, bubble traps are usually used just before the return chamber to control the amount of bubbles getting into the pump, you should only have a baffle after the skimmer to control how high the water level should be in that chamber. hope that makes sense lol but i could also be reading your design wrong too
the other problem is the size you have set out for your return area, if it is only 3.5" the largest hole you will be able to safely drill would be like around 1.25" ie 1/2 inch bulk head. just reminder, if you want a one inch return, than the hole size is almost two inches. now also keep in mind the hole also has to be half the diameter for the hole from the edge of the glass to be safe.