I'm about to do the same modification/fix to my v6.
I currently have BBK shorty headers, and Pypes bombs axlebacks. The o/r x-pipes are in the air from Lethal Performance.
I'm happy with the deep "sound" created by the Pypes axlebacks, but i've recently been invited to track days, and feel I needed to remove my cat/mid-pipe for more performance.
There is a guy on youtube that installed 18" resonator glasspacks on his sixxer. IMO, It sounds deep, smooth and rasp free. 2011 Mustang V6 Roush Exhaust + 18" Glasspack Resonators