I checked out the pipes and didn't find anything obstructing them. Maybe the previous owner had already pulled it all out at some point. Regardless, my goal was to get the '08+ exhaust on my '06, and it is now complete. So for all those who have wondered if it can be done; with a dremel, some welding skills, and a lot of patience it can. The entire midpipe even bolts right on. I'll get some better looking pictures once it's all back together.
Now I'm just waiting for my Woodcraft clip-ons to come in.