Mirza,
When you stopped mysql after prepare stage. It was clean shutdown ? My assumption is mysqld was not stopped cleanly.
Error log points that too.
[ERROR] Can’t start server: Bind on TCP/IP port: Address already in use
[ERROR] Do you already have another mysqld server running on port: 3306 ?
[ERROR] Aborting
Further, when you started mysqld after copy-back does it started OK or it fails to start ?