Lost all settings

I hope I have posted this question in the correct forum. Earlier this morning my toddler managed to drag all the files out of the Library file and resdistribute them around the desktop and into other folders in the HD including my user area. I realised the full extent of the damage when my e mail wouldn't work and my iphone couldn't pick up my music library when I tried to use the remote.
On further investigation the Library folder seems to have duplicated itself and added files to itself - the computer will not let me put the original back - it says I do not have sufficient authority.
I called the technical support line but they were not very helpful and said 'don't muck about with your library'.
I have managed to get my email working again but cannot retrieve saved emails.
I have managed to get the music back in itunes but still cannot get the iphone to work remotely which suggests that it is not all in the right place.
More alarmingly following a restart of the computer it has lost all of our settings - no personal documents, photos etc any more. Can still use itunes and mail but not remotely.
Can I restore anything by doing a disk repair or am I barking up the wrong tree? To be honest I would just like itunes to work properly again but am concerned the problem is hiding more problems.
Please, any suggestions welcome. We know we have been silly and when this is resolved we will start to back stuff up and also put on a password to protect our stuff from little fingers - we were so proud of her mouse skills ....

Hi, see if this helps or could be the case...
Return to default desktop, apparent "loss" of home directory...
http://docs.info.apple.com/article.html?artnum=107854
ChangeShortName 10.4 only...
http://www.macupdate.com/info.php/id/16620
Tough call on the Repairs, which I normally recommend, but in this instance I'd wait.

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