Hey Jonathan,
So when I setup the Boolean Modifier for the gun to cut out the barrel it adds the object I am trying to cut out rather then take it away.
I have tried many different things and I am not sure how to fix/get this to work.
Interesting! My first thought is maybe the normal for the Circle object are backwards. If that doesn't fix it, and none of the other operations will do it, try to move it around to see if for some reason it's having trouble calculating in exactly that position for whatever reason. Hope that helps!
So I made sure the Circles and the object's normals were properly calculated and they were, so I then moved the circle around and even put it on a different object to see if it would work.
First Image, I just moved it onto a difference spot on the first object, still didn't work:
Second Image, I put it on a different object and it cut, but it just cut a circle and not the rest:
