I have gotten a few emails on this, so I will post here... I have the BD 4" exhaust, so I have not tried to mount these flaps on a stock system.
I would crawl under the truck and see what would be best... extend the pipe before it turns out, have a shop lessen the bend in the turnout, or something else.
You might also try watching signatures for someone with these flaps and stock exhaust to see how they did it. I can tell ya that I really like the looks and functionality of these flaps... an exhaust modification, if needed, is well worth it.