Help Required - Ran "Repair Permissions" and lost files

I was having a few unknown errors with my computer lately... (iBook G4, Purchased November, 2005) I was unable to print, OS 9 was not loading, and everything was really slow.
When looking around in my computer (Only been using a Mac as long as I have had this computer), I found the disk utility and figured that would be a good place to start. After running the "Repair Permissions", I was pleased to see my computer was running quicker, and my programs were opening properly.
Now...The problem....
I used to have a fairly cluttered desktop...and as of a few weeks ago, I took everything, and put it into a new folder in the Hard Drive. After the Repair was finished, I found that particular folder was deleted. My Trash was still empty, and when searching for that folder, sub folders, and programs there, they were no where to be found. Also, it appears it was only this folder (It was called Main Directory if that helps at all) that was deleted.
I have noticed, that a few of the programs deleted do have files in the "Cache" folder....But I don't know what good that does me.
Any help in recovering these lost files would be greatly appreciated
PS. Yes....I have learned now not to poke around and run utilities that I don't know what they really do...at least without backing up my hard drive.

I'm sorry.....I made a mistake...I got the computer 2004.

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