Got new iPhone, tried to move iTunes library to different iMac, no luck?

OK, so this is a complicated situation. My wife and I went out to get ourselves new iPhone 5s today. When we got home, we discovered that our laptops, which we had been using as our backups on iTunes, was considered out of date. We already traded in our old iPhone 4's at the store to get discounts.
So we looked around and learned that we could use an external hard drive to transfer the entire iTunes library to our desktop iMac, which is much newer and less than 2 years old, with Mountain Lion installed. I copied my wife's iTunes folder as instructed, and moved it to the iTunes folder on her personal account on the iMac. No problem.
My wife then went ahead and plugged her iPhone 5 into the iMac. We ran into some troubles such as authorizing the iMac to accept the purchases and so forth, but while we were doing this, we noticed that the last update had been 2010, when my wife had her 3GS. I thought that wouldn't be a problem, and even made sure that the correct iTunes library was selected by pressing option key while opening iTunes.
So my wife syncs her iPhone. Alas, iTunes went to the 2010 backup. However, when I press on "Apps" on the iTunes store, it shows all of her current apps from her iPhone 4. It also shows some of the books in iBooks that she saved. We have NO music files at all since we are deaf. Her contacts list is not showing on the iTunes, though.
Did we make a major goof here? Our laptops still has all the iPhone 4 info - how do we get that from the laptop's iTunes to the iMac iTunes, and then from iMac iTunes to the new iPhone 5? We thought doing the external hard drive way would be OK - it does seem to have transferred all the info but iTunes on iMac is acting like the last update was 2010.
HELP!

http://osxdaily.com/2009/09/11/iphone-backup-location/  - "in Mac OS X your iPhone files are backed up at the following location: ~/Library/Application Support/MobileSync/Backup/"
in OS X:
~(your home directoy)/Library/Application Support/MobileSync/Backup/

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