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That's odd... The file was literally a single contiguous 2D shape which was extruded. So it shouldn't have any bizarre geometry there. I sliced mine in KISSlicer, I haven't tried it in Slic3r so I can't comment. Perhaps someone else here has used it to slice the files.

You could try passing the STL through Netfabb free, or use the netfabb cloud service (which I've had good luck with STL wierdness, it seems extremely good at repairing even the most troublesome STL files).

The netfabb cloud service is at

Hope you get it to print!