My Ipod Touch AND my itunes are apparently broken

My iPod touch crashed while I was updating an app from app store. I had to get it to shut off and then turn back on with the white apple loading for 5+ minutes.
Then when I access my ipod touch, some things are arranged differently than I had them before. Also, now it seems I have the ability to cause apps to disappear (even the default ones like weather and stocks and itunes) by putting them on the 9th page of apps and putting another one on page 9, thus pushing the last one off onto a non-existent page ten.
I realize this is a problem when I see that I've accidentally knocked my App store app off onto this unreachable page ten.
So I figure I better sync my ipod touch and try to fix whatever is wrong.
Not going to work because now my itunes library is all fracked. See, I have been trying to save room on my laptop by transferring my itunes and itunes library onto an external hard drive. I deleted every scrap of itunes related things off my laptop hoping that when I sync my ipod I can simply access all the itunes material I have saved on my external HD.
I load itunes from the external HD and nothing is on it so...ok, I decide to open up the itunes folder on my external HD and physically drag everything into my itunes program before syncing my ipod again. It loads everything, even things I had deleted previously. It now doesn't match up at all and I am not even sure how to begin to make it exactly how it was.
I try to sync my ipod touch anyway to at least try to correct the problems I detailed at the beginning of this post. ...and I get an error message that my ipod touch is synced with another itunes library. An ipod can only be synced with one library at a time. what would you like to do? My options are "erase and sync" which replaces contents of the ipod with the contents of the itunes library. or "transfer purchases" which copies purchases this computer is authorized to play from this ipod to the itunes library. I don't think transfer purchases is wise. but "erase and sync" seems dangerous.
That seems like I would lose anything I downloaded onto the ipod since my last sync like 2 weeks ago.
At this point there are so many levels of failure that I am not sure what to do.
Any ideas out there? I know this is convoluted but I am sure someone here may be able to piece some logic together from it. Or is my ipod touch basically stuck on whatever I happen to have on it right now?
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UPDATE: I soft reset the ipod touch and now all of the apps that disappeared onto the mysterious page ten are now back. However I just now consigned "Stocks" app to oblivion once again so I guess that page ten still eats apps if I squeeze anything onto page nine.
Also my issue with itunes and syncing to this new library is still a problem.
Will I lose all my apps and, for example all my downloaded books for Stanza and ibooks if I were to select "erase and sync" with the newly formed itunes library on my external HD. I have been setting that library up and everything that was on my ipod is in here. But I don't know what the locations all my apps and the preferences or my books in my stanza or ibooks. is all of that self contained in the .ips files?
also, there are only 51 items in my mobile applications folder when I have over 100 apps on my ipod touch....so I guess I am screwed out of over 50 apps files since I can't find them to add to my mobile applications folder for syncing.
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