I have a Gibson Flow thru muffler on my 2 door (as well as the air raid cold air), since I crushed my factory muffler coming down a water fall rock step.
And yeh I added a 1/4" steel skid plate over the Gibson now too.
It tucks up nice and uses the factory pipes but does make a difference in the power curve, tho not nearly as much as the cold air does.
It adds a nice throaty growl to it that isnt overpowering or annoying to neighbors but does sound really good especially when firing it up.