Well, unfortunately there is currently no ideal solution for this requirement. I would suggest setting up the iPads without iCloud sync and then initially restore a full backup from your main iPad to the other iPads. Once this is done, replace the pdf files for whatever you need.
After this initial setup, use playlist exports instead of backups. So create your setlist on the main iPad and export the playlist as an stsa archive with all files included. When you import this file on the other iPads, it will ask what to do with local versions of these songs and here select keep the local files. That way any new songs would be added but existing songs with custom pdfs will not be changed.