Keith,
What you posted makes perfect sense, but unfortunately, the pump (Eheim 1046) arrived at my home today. Since my tank doesn't have much SPS, I'm hoping that the bubble count will be low enough so that I don't run into too much trouble. I'll find out after I finish the reactor.
Steve,
I glued the flanges to the tubes. Bought most of the fittings but was waiting for the pump to arrive. The holes on the bottom flages sealed up fine with acrylic scraping and weldon 4.
I ran into the first "if I were to do it again". We should have drill for the holes for the tee eliminator a little smaller than 1". After sanding, the hole is a little too big for the tee eliminator and is causing a little drip. I'll need to add silicon around the edge.