Lost 3rd Party Apps After iOS 5.1.1 Update.

I updated my wife's iPhone 3GS from iOS 3.something to iOS V5.1.1.
This device had never been connected to the computer I used. I download iTunes, authorized the iPhone, downloaded iOS, did a backup (by right clicking on Device). I think most, if not all, of the apps that have been added to the iPhone were not downloaded from the iTunes store.
I did a transfer (which I think puts the apps into an iTunes Library). I was warned to authorize the this computer for iTunes store purchases or "41 apps ... would be deleted". I authorized and transferred. The apps Library display showed 41 apps.
I performed the update (which also did a backup). I was careful not to disconnect the iPhone until the iTunes summary page showed that the iPhone had been updated.
The 41 apps are not on the iPhone. I selected all of them in the iTunes apps library and did a sync. Still don't have those apps on the iPhone.
How do I get those apps from the iTunes Library to her iPhone?
DISCLOSURE: I am not very iPhone/iOS literate.

You're Welcome... glad it got you off the couch...
In case you need it... See here for detailed Syncing info...
http://www.apple.com/support/iphone/syncing/
From Here  >  http://www.apple.com/support/iphone/
Cheers

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