I found on Windows that I have to run apply_amps as administrator. Is it possible root is required for *nix (I presume you're using *nix since you list the .sh)?
For my test environment, I just make copies of the complete WAR files outside of tomcat and label them as "bare", "withxamp", etc. Then I can swap them in/out of webapps (shutting down tomcat, deleting the expanded code directory, restarting tomcat around it). I'd be very cautious on a production box, it would be easy to make a mistake and break customizations (or worse, lose data)!