ITunes stopped working and now all of my apps for my iPhone and half of my music is gone. How do I get it all back?

I've recently upgraded to an iPhone 5, I had just restored my old iPhone 4 to its original settings while listening to my music. When that was finished I plugged my new phone in and I had an error message pop up saying "iTunes has stopped working" and had to close it. When I reopened iTunes all of my apps for my phone were gone along with half of my music library. The only music I have left are the albums I have downloaded the rest is gone. I closed and reopened iTunes several times and got the same message each time.
I have music and apps on the phone which will not transfer back to iTunes. All iTunes does is ask if I wan't to delete the music on my phone and sync with the library........ silly question really as half of the music in the library is gone!
I have been using iTunes for many years now and this is the first time I have seen an error such as this. Can anyone tell me how to restore my library to the same as it was? I have fixed the "iTunes has stopped working" issue and would like my music and apps back.

See this post.
tt2

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