In order to maintain multiple schools running Open Admin, I have done the following:
An upcoming version will have to take into account modifications to a file that are specific to a school. (ie. customization). If those changed files are placed in a directory at the school level (ie. same level as etc and cgi) instead of where they normally run and then a symbolic link added to the normal folder pointing to the custom folder, a new oafscopy.pl script could detect the presence of the symbolic link and not copy the update for this school (although it should warn the user of this event).
In the Notes folder, mentioned above, I place notes to myself about particular settings in each school, any customizations for any school, etc. This is particularly important for student numbers since I assign each school a particular range of student numbers (which is stored in the /cgi/entry/studentnumber file). I use a large range to that this setting would last at least 6 years or better. At that point, a centralized (per division) routine can be used to assign division student numbers. For now, this method of storing the next available student number in a file is simple and reliable.