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maybe I'm second guessing my self and one wont be needed however it's my gut feeling and I work a lot on these it's going to be better to have more flood and drain cycles than less. Will have to work my way through it.
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Ya, observation is key. Adjusting to what you see is very important. As well as the key to learning. Going by the pictures, I don't know if you have a overflow system or not. Typically a flood and drain system does, and would solve your timer issues if I understand correctly.
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As you can see from the pics I'm using two 100 Litre plastic containers for my resivours and have a submersable pump in one and will route the overflow back to the second one use the full capacity of nutrient in both drums. Would be easy to fit a solinoid controlled valve to have to system drain back to the second drum if I feel there is need to do so.
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I had a similar system setup using two 32 gallon trash cans for the reservoir. I used a siphon tube between the two containers (Just a 8 foot piece of garden hose) one end in each trash can. Water seeks its own level. So as long as the pump does not pump faster than the siphon can replace it, the water level will remain level in both containers. As long as the tube is at the bottom of each container, so no air bubbles will be able to stop the siphoning action. No electronic parts to fail, or run up electricity either. Just weight down both ends of the tube to be sure it is at the bottom.