I realize this is an old thread.......but.........
The solutions I see here are not unlike a person with a rock in their shoe. Because of the rock, their foot hurts....so they take an aspirin. Seems like it would be easier to get rid of the rock.
If you have flies, the first question to ask is why? What is attracting them? Get rid of that and the flies go away. A shop vac? Really?
Most likely what is attracting them is a combination of wet, spilt feed and droppings. If on mud, that doesn't help either. To the extent spilt feed is involved, the right feeders will help. After that, deep litter (at least 6 inches + to start) will go a long ways towards helping with the fly problem. Best deep litter I've found is old grass hay. But old leaves, pine needles, grass hay and wood chips etc, will also help. Something that was once a part of a living plant that when combined with the Nitrogen in the droppings, will combine with the carbon in the plant to start to decompose both. A cold compost process. Healthy living.
Smell goes away, as do the flies.