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Wow.. I spent a while staring at that. :)

I'm not an expert either, but it seems that dropping the high flow pumps to the bottom of the "live water" tank would help with bypass. Also, this reduces the chance of those pumps getting airlocked if the water level in the "live water" tank drops, due to evaporation or failure to fully refill the system.
 

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The reason for the pumps being at the top and not at the bottom is an overflow concern. If syphon was lost at the tanks, then water would not return to the bucket. The water would continue to pump out back into the tanks, which would then overflow. By having the pumps at the top of the barrel, only a small amount of water can be pumped back into the tanks. This would not be enough water to overflow either tank.
That leaves a small margin between the amount of water in the system that would allow an overflow, and the amount that would cause an unnecessary shutdown. Going through all this trouble to build a system that ultimately proves overly sensitive would be disappointing.

I'd rather allow the pumps access to a greater portion of water in the "live water" tank, and rely on mechanical float valves, or electrical float switches controlling the pumps, to prevent a pump overflowing a tank if the siphon failed. It would still be able to overflow a tank, but only if two failures simultaneously occurred - a float valve/switch and a siphon.
 
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