Let me try to answer but others may have a better suggestion, so here goes:
1] You can run “–apply-log --export” during the prepare phase so as to create those .exp and .cfg files needed when importing the individual tables. You can read further here - [url]Percona XtraBackup. This is going to be a tedious task in case you plan on importing a lot of tables.
2] There is no exclude option but i think you may be able to use either --databases or --tables-file options, of course you should not include the database you want NOT to be backed up in the process. For further reading - [url]Percona XtraBackup
3] There is no specific rule on whether you run --apply-log after the backup was created or before you want the backup restored. BUT, to make sure that your backup is valid, you can run --apply-log to check it. To understand what --apply-log does, please refer to [url]Percona XtraBackup, since --apply-log implies running xtrabackup --prepare twice.