Hey Jeff,
The installation script is only for new fresh installations. If you are upgrading the app then you should not run the installation script at all and update the files manually.
If you want to install the version 3.0.0 first and then move your code to that version, I would recommend you to use a different database for it. The database structure is the same in those versions and you can always easily change the database you are using inside the configuration file.
- Milos