... an issue replacing bulkheads in a narrow overflow like this...I also raised the open channel a bit.
Minimum clearance inside the overflow, front to back should be where there is enough room for the bulkhead to fit before it is pushed through the hole. If you cut the threaded portion of the bulkhead to the minimum leangth that still leaves enough purchase for the nut on the backside, that would be the clearance you need.
Unless you raise the open channel to where its lowest point is above the highest point of the siphon, I don't see any functional gain.
I will be making my overflow from acrylic and will be a full box as in the picture. The box will be held to the DT by the bulkheads. making the shelf removeable for cleaning is a good idea. Regarding vortices, I think I remember reading somewhere in the thread that they are not an issue do to a combination of the small volume in the box (made even smaller without the 90s), the turbulent flow in the box and the proximity of the opening to the wall of the box. The last factor does not come into play when the 90s aren't used but maybe adding another baffle that could be slid into place after installing the bulkhead could be done if necessary?
After a certain point, it becomes an exercise of overthinking the solution to a problem that already has an answer... but I supose that's how we got the current answer in the first place.
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