Well the 90 is going to be a fish only tank, so do I have any other filter options besides LR? How about a hang on tank filter? As for the 1" sand bed, I have had a 1" sand bed in my 90 for over a year and the nitrate is zero. I keep very few fish in the reef tank and the fuge has a lots of cheato.
If I take out the bioballs do I have to refill it with LR rubble? Does the rubble stay in the compartment above the water? Can I just let the water rain down into the sump without anything in it?

The main problems I see is that I cant move LR from the 90 into the 180 without disturbing the corals. And I cant move rock with coral on it because the nitrate is high in the 180 also the butterfly will eat most everything. If I can get the 180 nitrates down to at least 10ppm can I move it all in and transfer the coral eating fish out in a day, without killing everything?