Thank you for the post.
The process is not as simple as a copy and paste because of Mac OS X permissions. I would suggest reading the entire chapter you mentioned in the FileMaker Server 13 Getting Started Guide.
From Chapter 6, Step 9. Move files to the proper location:
“Move the script files and plug-ins you used with the previous version of FileMaker Server to the proper folders within the FileMaker Server 13 folder structure. See “Step 4. Make a copy of databases, scripts, and plug-ins” on page 62.
Note: You can use FileMaker Pro 13 to transfer .fmp12 databases to your new FileMaker Server deployment. See “Uploading databases” on page 53. To transfer your database files manually, see FileMaker Server Help.”