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I had rots on the floor before, during construction, you can siphon as long as the container is at the same level, you are only removing less than half the water anyway...
Have you drilled all the tanks? The only problem i see with your overflow is that that type of set up is not very good at removing oils from the surface. Stand pipes are better at that. The only thing you can do is attach an elbow to the "bulkhead" but the hole is to close to the edge and will overflow.
Ed
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