So, now you know why everybody always tells you to make a backup of all your data before you change your setup.
First, do some damage control, and backup whatever is left of your data files.
While trying yo recover you are bound to make more mistakes and one of them will erase all that was left of your databass.
Then start by reading the F'ing mysql manual on how to setup InnoDB support:
http://www.mysql.com/doc/I/n/InnoDB_start.html
http://www.mysql.com/doc/I/n/InnoDB.html
Then pray MYSQL is wonky enough to let you replace the newly created innodb file with your old one.
Oh, and if you do get it working, please make a backup of the data so you won't have to go through all this again.