Syncing ipad to a new computer

[Thescatterling]

My old computer died and I'm now facing a problem. I need to sync my iPad to my new computer but I'm not sure if it's possible to do it an still save all my folder settings, bookmarks and so forth. I have over a thousand books and numerous work related PDFs that I've spent hours sorting into their appropriate folders in the iBooks app. I've moved the files into iTunes on my new computer and downloaded all my apps. Is it possible to sync my iPad to my new computer without completely wiping all my settings? Google has not been helpful in this respect. I've put it off for quite a while now, but there are some books and music and I'd like to sync. Please help me!

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[Thescatterling]

The main thing for me is NOT losing all the folders I set up in iBooks. I spent hours organizing it, and I would rather beat my knees with a hammer than do it again. Not all my books come from the apple store, in fact most of them are my non drm epubs.