part of the problem is the type of file insert it was to begin with. At this point (I'm moving data so can't do anything specifically for you at the moment), you still need to tell the thing to stop running.
I also found out something interesting last night, and changed it, so hopefully this will help where there is an issue. Years ago, the database was set to where the chapter data insert was set to "longtext". At some point during the time the data was being restored FROM the crash, it was changed to "mediumtext". What this did is make it so long chapter inserts are continually trying to truncate. Mind you, I was in the middle of moving chapter data, and kept coming up against that. As the database accepted it at the initial upload, I thought there had to be something else at play. I checked with the other gal (who was around for the crash, but not during the restore), which is how I found out that the field properties had been changed. So last night, I changed it back.
You're using IE, if I remember correctly, yes? You do need to make sure that it's set to accept 3rd party scripts and addons, or it will not behave well with java apps.
I went through the chapter records for your stories, and what I found was illegal div tags which called for things which don't exist on this site. That is very likely the cause of the problem.