Yes, you've committed the cardinal sin of iPhoto:
Don't tamper with files in the iPhoto Library folder from the Finder.
In your Originals folder should be all of your full sized image files. At least that's where iPhoto starts out saving them. What you need to do is somehow find all of your full sized files that are in your iPhoto library folder and move them to a new folder on the desktop. If you have some that are the same name you'll have to move one of those to a different folder. Your Originals folder should have all full sized image files. If you didn't move any files from the Data folder in there just move it to the desktop.
You can also move any files in the Pictures folder that are full sized into a new folder on the desktop.
Now move the iPhoto library folder to the trash. It will not be needed. Next launch iPhoto and when it tells you it cannot find the library select the option to create a new library. When that is done you can drag the Originals folder from the desktop into the open iPhoto application window. It will import all the files that were in that folder. When that is complete you can drag the other folder (the one with the other image files from the Pictures folder) into the open iPhoto window. When those files are imported and you can see you have all of your photos in that library, you can move those two folders to the Trash and empty it.
Now you can go about arranging and grouping your photos from within iPhoto. If you select a number of photo from the main library window you can use the menu option File->Create Roll and put them in a roll of their own. That roll will be represented by a new folder with the same name as the roll in the Originals folder. You don't have to go into the iPhoto Library folder via the Finder at all. All file management should be done from within iPhoto, i.e. creating new rolls, albums, etc.