My biggest problems with the overall designs:
1. Horizontal filter - any way you can turn the whole cyclone body so the fiter is through the wall on the left? I don't think you're going to be too happy with it laying in the ceiling.
2. The ducts break plane - meaning they to up, then down and across, before going back up to then come down to the unit. I know the ducting takes up space but by just ceiling mounting (below the joists) you eliminate the up-down-across-up-down. You can also run wyes along the ceiling to create more than one run.
3. If the walls between the rooms aren't structural I would take them down so you have one continuous space (be easier to ceiling mount ducting too).
-- John
"No matter where you go, there you are" -- Buckaroo Banzai