In case you didn't know, when you boot up, a background process begins restoring symlinks. If you have loaded up your Z with lots of packages (lots of files), the process can take quite a while, during which time certain things wont work. My strategy is to install most lib packages in /, that way they are always present. In addition, any network type applications also go in / as opposed to on a CF card, since sometimes you may want GPS or WIFI in the CF slot.
Also, if you are not compiling stuff, don't put gcc headers and the other tools on your Z. That's a lot of files.