If you only need the html version, you can use this temporarily:
http://localhost/fflag/getstory.php?...toryid=3928537
At least until erayd gets his server all fixed up (it's down again for me). It's easy enough to convert from html to epub using Calibre.
Unfortunately, can't help you with the Mac problem as I'm unfamiliar with both Mac and Linux.
@erayd
FanFiction.Net changed handling of crossover fanfics. The code snippet above (for the ffnet_get_meta function) should fix it, except, mobileread automatically substituted the >> character instead of showing the html entity. Are you sure svn r29 still works for you? Because right now, there's an extra <img src='/static/ficons/script.png' width=16 height=16 border=0 align=absmiddle> in between <td> and <a href.