I'm in the same boat as I plan on eventually going with headers while keeping my PE (because it sounds great, is built well, looks great, and is the only option other than stock that retains the box's shape for aero). Would love for you to be the guinea pig.
I've been looking into a couple of ideas... I'm thinking a straight-through muffler/'glass-pack' on the PE mid-pipe will be the best option, I'm just trying to decide on a good one that will fit. I'm curious about going back to the stock resonator but I doubt it would make a huge difference.