Great thread. Took me days to read!
I have three quick questions:
Do right angles in hard plumbing affect flow?
Should the fuge/cheato reactor be the first in line from the overflow water?
How do you manage multiple reactors with different flow requirements?
I believe you'll see a flow reduction in anything unless it is a straight line, 90's more so than 45's. The question is how much and will it make a difference. I have the @Crystal Reef Aquatics triton sump and the refugium is the first chamber, if you plan to use a reactor I don't think it will make much difference where you pull the water from. As far as managing flow you can run a manifold off your return pump and use valves to control flow to each reactor. Alternatively you can use a return pump for just the return and an oversized pump can run your reactors, you'd still create a manifold and use valves to control the flow.