Really, you don't want to recompile every copy. You want to have the config data outside of the compressed fs. Or, since your data is under 400mb, you could make the whole CD uncompressed.

Btw, I suggested something like what you are doing in the past in order to make customized versions of Knoppix (with the user being able to select on a webpage which applications his Knoppix CD should contain). So I would be really interested in your server-side scripts. Which languages do you use? A combination of PHP and bash seems a good choice.

Would you be willing to release your server part under GPL? Then probably people would be much more willing to improve it and optimize everything...