I have just downloaded ios 7 and now my ibooks is not me default PDF reader. It is not recognised at all when it comes to using a PDF file and this is not good as I have folders on ibooks which I wish to add to but now cannot

I would like help as I cannot find another app that works where it will store files in folders

I have no idea what may have caused your MacBook to stop working, but from your description it kind of sounds like it may have started before you ran Software Update and installed the new Apps. Just the general slow feeling and bugginess is what tips me off. You said that you weren't sure if you had closed all open windows, that doesn't matter if the computer restarts itself. It automatically closes all other open applications when restarting.
As to your data being retrievable, if when you take it in they do a fresh install of the OS, then no, it will not be unless you want to pay several thousand dollars to a software retrieval company.
I am glad to hear that you have taken into the Apple Store to get it fixed, and that you have all of your purchased music backed up to your iPod. You should be able to just transfer it all back to iTunes once you get your computer back should it be necessary.
As a side note, the proper place for this topic would probably in the MacBook forums, not iTunes since there is no evidence that iTunes started the issue.

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