My plan at this point is to set up both new tanks as totally new and not trusting anything from either side. If the red side does survive until the new tank is ready for them, they will be acclimated to the new tank and the old tank will be taken apart and sterilized.
I never did want the water to be drawn through the foam as a filter. That would require regular cleaning, which would mean uprooting both colonies during maintenance causing too much stress. I basically just wanted 2 - 5 gallon tanks that for stability would act like one 10 gallon.
Looking back in the history, I did use Flourish at the start of the colony hoping that it would help the Marimo Balls & Java Moss grow better, which I believe it did.
I have about 3 weeks before I can put the new tanks in place on the rack. I do have an extra 10 gallon tank. I might start cycling (fishless, of course) that tank while it's on the floor now, with all the new filters, then just transfer the filters into the 20 gallon tanks when they're in place for a quicker cycle. This time when I start the 20 gallon tanks, I will have better lights & more plants to keep the Nitrates in check better. Live and learn.
Just a quick question, how large of a tank do you have? You said that you do about 10% per week, how long does it take to refill your tank? When I was doing 10%, I would drip it in for over an hour for 1 gallon. Then I started increasing the amount and the speed and it never seemed to bother the shrimp as long as the water temperature was matched.