Updating iPad 1 to 5.0.1, seriously?

Over the last 24 hrs I've been in the process of updating the software on my iPad to 5.0.1 from 4.2.1 (if I remember correctly). Naturally, I wanted the state of the iPad to remain the same, i.e. media files in place, apps in place, app data in place etc. So, I follow instructions:
upon plugging in to same computer as used for configuring, prompted about transferring purchases. I go ahead and do this, using right click on iPad icon in left bar, but for some reason, the prompt keeps coming back, so I hit it a few times before growing very tired of this prompt, and assume it has been completed. So my first question is, why does this keep recurring, and why is there no way for me to determine what remains/has been unsuccessful?
I start the update cycle, which prompts me to back up, which I do (this takes a while), then update, then it automatically restores. IT'S JUST THAT THIS RESTORE ONLY RESTORES A VERY SMALL PORTION OF WHAT WAS THERE TO BEGIN WITH. So yes, some of my purchased apps are there, but most aren't. Most of the media content I had on there is gone. The worst part is, I'm not the only one using this iPad, so it's hard for me to recall what other family members had on it. How could this happen? Why did I spend >1 hour backing up the device? Where is that backup, and how can I find out what it contains?
I'm now in the process of redownloading/reinstalling the apps I can remember having on there, but my guess is that for those apps that were "lost" in the process, their app data will be gone. This includes data such as recordings of my wife, a composer, which was only stored on this device.
Sorry about the frustration, but this has easily been the most angering experience I've had with a computer.

You should be able to simply sync with iTunes again in order to reload all of you apps and media. That is why iTunes prompted you to transfer the purchases. You may have to select all of the content again when you click on each tab in the iTunes window on the right, but the content should be in your iTunes library.
You should also be able to restore from the backup that iTunes created before the update took place in order to restore your app data. When the iPad is connected to your computer and with iTunes running, right click on the iPad on the left side and select "Restore From Backup". A window will popup with a drop down list of all of the available backups for the device. Select the one that you want to use and restore from it.

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