Could you simply use a config script on the cd's, which is outside of the cloop, to make the customisations? Even better (ok this is a lot to ask but perhaps you would be able to do it) you could default to taking the config from a usb key so that they can use the stock iso and tweak the customisations themselves without having to give you the usernames and password (you could probably even customise it to prompt them for the values for the config to do this if it finds a usb key without a config setup, so they never have to give you any details). You could also setup the remaster to automatically look for a persistent home (on the same usb key) so they/you can klik in extra apps and carry around useful/important/sensitive files (I'm sure you can use encrypted persistent homes).

Perhaps you have requirements that can't be met by this though?