Let me ask you this. Why do you want a canopy? Unless the tank has to go in a more or less formal room like a living room, a canopy really gets in the way of working on the tank, and if you have lighting mounted in it, makes it even harder to deal with. I'd say either shipe the canopy entirely or make it strictly decorative, mounting the lighting by other means.
Note that many LED fixtures mount from cables or to brackets tat attatch to the tank or stand.
As for exactly how many fixtures you'll need that depends a lot upon the lighting effects you want in the tank. For a rough estimate you can figure each LED fixture will cover about a 2 foot length of tank, but this can vary depending upon the fixture, it's lens system and what your trying to do with the lighting.
Building a tank into a wall can look fantastic, but if you ever decide you don't want to have an aquarium anymore, you have a hole in the wall and a small room you might not be able to use very well. I'm not saying don't do this, just consider long term.
Maybe just personal preference but i would push the majority of the flow into the protein skimmer section and place the return after that. You could minimize the flow through the refugium and then divert into the return.
There is a lot to be said about the cost savings and Practicality of making your own out of a 40 breeder with some baffles. Fancy designs don’t really do anything and you can invest the money elsewhere.
Personally, I’ve owned a diy 40. A lifereef sump and one from advanced acrylics (current).
due to my current size and needs for connected devices, I had John at AA make mine, and I like it.
DIY is pretty simple., but if you have extra $$ i would go with manufactured just because you usually get a lot more details built in. Especially if you have plans for dosing, or probes etc...
Bigger is better either way, as long as it fits your space.