The problem you are seeing with Aristotle is a result of using the wrong
version of the Apple II Setup. You have to use Apple II Setup v2.1 or
2.1.1, not v2.0.1, when setting up the software.
As for the problem of installing 6.0.3 from the File Server installation
disk, it could be that there is something corrupted in the installation
scripts for that version. Nothing you described is a wrong procedure.