Lost files after reboot

Last night I was having speed issues and things with my MacBook pro, which is 2 years old. So I shut it down for the night to let it rest. When I woke up it would start past the startup grey/blue screen with the apple. So I looked up things to do about this and I ended trying a bunch of stuff.
I reset the PRAM, I held option and selected what I thought was my normal Macintosh HD but now I'm not so sure. I also did the whole fsck thing until it said it appeared to be okay. Finally I held shift and did the safe boot thing and that got the thing going and it turned on.
But when it turned on google chrome had no bookmarks and my folders were gone from my desktop and m iTunes was empty. I thought I had somehow wiped my hardrive but all the items in my trash were still there, the files in my downloads were there, my Mail accounts were perfectly fine and some documents were still there. I don't know what I did. I tried the option start again and the Macintosh HD is labeled as EFI something or other.
Any help or ideas would be greatly appreciated.

luke.un,
you can restore your missing files from your most recent backup. If you haven’t been making backups, you can hire a data recovery firm to see if they can get those files back — but note that their services tend to be expensive.

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