Warning if you reset the filters on Mass Storages the first dust that enters will also set the dust size, meaning you effectively CANNOT use them that way you just thought you could use them. I was referring to that you can just let the Dusts go to their intended target directly by using Mass Storages as Filters everywhere in your System without caring what size the incoming dusts are.
Also as far as I know the Dust Funnels work Instantly and for Free, Boxinators cannot be faster than that, they can only be equally fast. You might be confused because the Item Pipes only ever send Items once per Second, so that is where your congestion comes from.
There is Plastic Item Boxes too, which are like Mass Storages but only store very very few Items.