The first thing I did was to replace the wet-dry filter. Instead of bioballs I use (from bottom to top) fluval biomax, filter floss (generic from LFS), fluval filter foam. I did retain the original filter cassett in section 1 just to keep the right water level. Make sure that the new filter is always covered with water - this means that the level of water in section 3 is well above Max line. The new filter has significantly improved water quality and unlike wet-dry will not degas CO2 from water - just make sure the water level is high enough to cover all of section 2.
Now my problem is that the stock pump in section 3 is too powerful and hot. Even with heater removed Biocube8 with lights on runs at 82F. With lights off it runs at 78F.
I plan to cover low intakes to allow for higher substrate levels.
I also plan to build CO2 diffuser connected to the water return.