There should be two amps. One is for Share, which it looks like you've copied, and the other is for the repository. I cannot tell if you've copied that one, which goes in your amps folder.
After putting each AMP into its appropriate folder, stop Alfresco. You cannot install AMPs while Alfresco is running. Part of the process is to remove the expanded web application directories and you should not do that when Alfresco is running.
Next, you copied the alfresco and share directories as a backup, and you plan to copy those back after installing the AMPs. Do not do this.
Any changes or customizations you've made should be in AMPs, so none of your changes are in the Alfresco or Share web applications. Therefore, there is nothing in there you need to save.
When you run the apply_amps script, it will merge the PDF toolkit AMPs into the alfresco.war and share.war files and it will remove the alfresco and share directories, which is what you want it to do. Then, when you start Alfresco up, Tomcat will re-expand the alfresco.war and share.war files into those directories.