ok i did a crude markup of what i can tell is happen, but there are a few area i am not sure what you had in mind
if you can tell me if this is close to what you had in mind or if i am missing something in this.
ok here are the areas that are confusing me
1)where the bubble trap after the skimmer does not seem to go any where
2)the water change chambers, what are they there for and why two?
3)it sound like you want to put gates values under water, i am not sure but i bet that may not be the best option as there is metal screws on the one that i have seem
4)what are you putting in the refug? a drop of 18 inches to even 10 inches for the water is going to make a lot of bubbles, that very close to where you return is