I'm having a spot of trouble following items through the "shuffle".
Perhaps one could divide the horizontal space such that each story gets it own invisible vertical band. A translucent coloured dot exists where the band intersects the story's present position. The dot traces a light line behind it from left to right. When the story falls off the page its band is collapsed. You know how long a story stays on the page so running out of space isn't a problem.
More simply, one could leave a single-period trail, with one terminus where the story was and the other where it is, persisting for only a moment after each shuffle.
Perhaps one could divide the horizontal space such that each story gets it own invisible vertical band. A translucent coloured dot exists where the band intersects the story's present position. The dot traces a light line behind it from left to right. When the story falls off the page its band is collapsed. You know how long a story stays on the page so running out of space isn't a problem.
More simply, one could leave a single-period trail, with one terminus where the story was and the other where it is, persisting for only a moment after each shuffle.