were you using textedit? i used textwrangler to edit it. its a text editor geared for people who code, and doesnt default to adding the .doc for saving files. i believe its a free download.

you could also save it as a .doc, and then change the extension later, and OSX will ask you if you "really" want to change it to .sh

Also, running 2 copied directories will slow things down, as the read head on the hard drive is bouncing back and for from 1 directory to the other, trying to read the same files, at the same time, from 2 different physical locations on the disc platters.