that will work great- its the shape and angle of the conical cyclone separator, the inflow angles and outflow- are all very critical- and Bill Pentz got it perfected over the years. Thats what makes bill's system the most efficient system out there, it removes more particles than any other system.
if its smaller, like you say, just empty it more often, but essentially it will be just as efficient as the bigger ones, just less capacity.
well done!!
ps, i think you can get the micro filters that go on the outfeed side- that will clean the air 99.99%.
use their filters as the wrong filter will restrict the outflow of air, then the inflow is compromised accordingly.