I love do-it-yourself projects! Saves money and you can be proud of you accomplishments.
I have a couple ideas even though I don't know much about that whole concept. It is an intriguing concept which would seem more natural looking than a skimmer.
Maybe you should ony have holes on the top. No holes on the sides or bottom. This way the pump's draw is limited on it's draw which may create a restriction and better suction. Right now it's drawing from many holes all around the box. Maybe less holes would create more suction. Sort of a venturi effect. Plus, I think what your trying to do is suck debris from the water surface. So why the need for holes anywhere but the top? You might also have to experiment with the size of the holes.
I'm also guessing a larger pump would be better.
I'm wondering how you would service the pump with all the stones on top. Sometimes they can clog from debris getting past all the stones, etc. I'm thinking you could lay some metal (not plastic or fiberglass) window screening on top. Then place your stone on the screening. Have the screening a bit wider so you can grab it from two sides to lift all the stone up at once. As long as it's not too much stone to lift. Then you can service your pump. Or maybe you can find something more rigid than screening. Perhaps hard plastic mesh of some kind.
Have the top of your box (instead of the side) removeable to gain access to the pump. I imagine you don't need much stone on top. Probably a thin layer.
You could just have a short piece of pvc out the side for your pump outlet.
Good luck...keep us posted. And thanks for the videos.