The junction is indeed right upstream of the cylindrical muffler, and it's a hybrid: one pipe is a slip fit and the other pipe is a standard "flange" type connection with two bolts, one on each side. I think... it was something weird like that. I chopped it all off and just welded straight to straight with no removable junctions. If you get fancy you could indeed weld it up with the appropriate removable joints. Oh, and cutting through the factory pipe was a major pita. I don't know what they make it out of, but it was some hard stuff. It ate my sawzall alive... had to break out the plasma cutter.
The X pipe sounds cool but if you get a 'co-mingling' muffler that joins both sides of the exhaust it'll accomplish the same thing, no?
Other than giving you a project, I don't see the advantage to rebuilding the entire system from scratch. You've already got nice tips from the factory SC system, the bends are right, the hangers are right, the alignment is right, etc... But knock yourself out!