I only flush once to twice a harvest, never had issues with that, even with other plants!
I some times need to travel for a month or so and need to have enough water.
Not everything is available or ever mailable where I’m at, I had to travel to get the LED lights, one at a time and still one more to go! 
How often are you running those pumps?
And what’s going to happen if one of those pumps takes a crap…
?
I think you have way to many variables and are definitely asking for trouble with this setup…
I think I could use everything that you already have and just change a couple of things that will put you on the right track…
If one of those pumps fail , then one or the other is going to overflow for sure… you need to be able to gravity feed back to your main resivor’s first off…
Second thing I think is happening is that your pumps are running way too much and heating up the water… not necessary… they need to be on timers that only run 15 minutes every 4 to 5 hours depending on how much water your new system that we reconfigure for you holds… 
3rd… you need to get rid of those big buckets… it’s a waste of space that your roots can take up… I would get new lids for the totes that you can cut in 6 inch net pots or stick with the 3 inch net pots and have more water valum…
I will draw you something up to explain better and you will be off to the races…
Up to you… ?
Your setup is in the right direction… we just need to put the puzzle pieces in the right order…
Pumps run 24/7 and water temperature is always stable at 18c/64.4, if a pump from either containers fails the other is able to still do the job and refill the reservoir at a slower rate, if both fail then the reservoir empties into the containers up to about quater if an inch before water level touches the plant pot! If the reservoir pump fails then gravity will keep the water running at less pressure.
I don’t mind making changes, im sure there’s much to learn and improve, looking forward to seeing your sketches
Ok… I get on it… I’ll set you up with what I think will be the best setup for what you already have…
