Need Help snycing apps from Ipad to new Computer

Need some help.
I recently had to reinstall Windows 7 After I had a virus. So I just installed Itunes and plugged in my Ipad to sync up my Apps since My Ipad is full.
But I been unable to backup my Ipad or transfer purchases to Itunes. If I try to backup my Ipad I get this message
"iTunes could not back up the iPad because the Ipad is disconnected."
If I try to transfer purchases, it looks like it is working as I can see it go through the apps in the top middle bar of itunes. But when I go to my Itunes libary it only shows a couple apps transferred.
Anyway to backup my Ipad on my "new" computer? I dont want to lose all my save files, bookmarks etc.

Tried multiple solutions and keep running into the same messages. I get the message when I try to back up and if I click on transfer purchases it seems like it works as in the top bar in iTunes it seems to go through my apps, it says coping but when I look in my App library they aren't there.
I really don't want to go through and try to download each app again. I have so many it would take forever.

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