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Setup looks odd to me from the pics as well. The one with a bulkhead down low could have been for a return line of a closed loop or it may have been used as a refugium that emptied into a sump right below it?
For what it's worth, I'm using a Mag 9.5 for a return on my 75G tank and I also have a ball valve on the discharge that's slightly closed (almost fully open) and it's perfect flow rate. I have a 1" drain pipe.