MySQL 5.5 : (InnoDB) - Manually edited an .ibd file to test recovery, now entire MySQL installation is broken!
Following these steps probably offers a decent shot at making the MySQL instance happy again... 


recreate the database's directory that you deleted
create an InnoDB table with the same exact column names and definitions and the same table name, but in a different schema (or on a different server)
copy only the .frm file for that table into the database's directory, not the .ibd file
be sure the file and directory permissions are correct
start MySQL normally (without innodb-force-recovery)
DROP TABLE database_name.table_name;


The server should then respond by removing the .frm file, removing the table from InnoDB's internal data dictionary, and return a simple warning that the .ibd file was missing.

You'll have to repeat the process for all of the tables, but if you have the schema on another machine (or identical tables in another schema on this one, already) you should be able to copy all the .frm files over in one shot, start up, then drop them all.

But don't try opening them, don't "USE database_name", and don't connect with a graphical client that tries to enumerate the tables.  Start the command line client with the --no-auto-rehash option so it doesn't try to enumerate them in the background, either.

This should let you drop the tables, at which point, you may be stable again.