What I know about cyclone separators is generally applied to solid separation, so take this with a grain of salt.
1. The Reynolds Number at the inlet needs to be above 2,000, but you’ll see better efficiencies closer to 10,000. In general cyclones are more sensitive to the densities of the media than to the pressure differentials.
2. To achieve the highest efficiency (about 95%) you want the discharge pressure of the dirty fluid to equal the discharge pressure of the clean fluid at the top of the separator. You can use whatever combination of piping, valves, orifice plates, whatever in the dirty flow obtain this (assuming that you can with this set-up).
I'm interested to learn what kind of seal and flush plan you are using with this blower. When I hear blower I am used to thinking of packing not a mechanical seal.