In FA 2.3 some tables are MyISAM and others are InnoDB.
In FA 2.4 all tables are InnoDB.
Since you were using a debian server - which version od debian and which version of MySQL were you using?
I just created a FA db with utf8 and persian collation in XAMPP v1.7.3 and then turned off the MySQL server.
I then replaced all files in the MySQL data folder's FA db folder with the ones extracted from your zip file and then start the MySQL server.
You can then use phpMyAdmin to do some diagnostic checks and repair if needed and identify the corrupt tables and replace them with ones from the standard sql/en_US-new.sql file after altering the collations.
All InnoDB table data files have only the .frm extension and none other. In some instances there will be some .ibd files as well.
Here are some references:
Ref 1 : http://www.fromdual.com/recover-lost-frm-files-for-innodb-tables
Ref 2:http://dba.stackexchange.com/questions/16875/mysql-how-to-restore-table-stored-in-a-frm-and-a-ibd-file
InnoDB tables cannot be copied the same way that MyISAM tables can.
Just copying the .frm and .ibd files from one location to another is asking for trouble. Copying the .frm and .ibd file of an InnoDB table is only good if and only if you can guarantee that the tablespace id of the .ibd file matches exactly with the tablespace id entry in the metdata of the ibdata1 file.
Ref 3: http://www.hexblot.com/blog/recovering-innodb-tables-ibd-and-frm-files
Ref 4: http://www.thegeekstuff.com/2014/04/recover-innodb-mysql/
Ref 5: http://egil.biz/how-to-recover-mysql-data-from-innodb/
Ref 6: http://www.bluegecko.net/mysql/recovering-a-schema-from-innodb-frm-files/
Do you still have the filesystem of the Debian server?