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Root [CDMA] Backing up/restoring apps

If you are not terribly worried about your settings in each app, appbrain will essentially save a list of installed apps to your profile where you can just load appbrain and it will automatically download and install all those apps for you. I think prety much any other method will require root.
 
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Recently my EVO 3D's mic was having problems and Sprint ordered me a replacement phone, which I got yesterday. I had used MyBackupPro to back up everything, and when I got the new phone I went through the annoying process of restoring the apps (choosing to leave some out). Next I logged into the Amazon App Store so all those apps would work. Then I restored everything from my Data backup (except the APN which MyBackupPro said not to do if I didn't totally totally know what I was doing, which I didn't). Included the Data restore is Android Home and System Settings. I did all the recommended Restarts along the way, of course.

But not everything is there. My wallpaper is fine when I open the phone, but the lock screen shows the weather, though 3 of my 4 shortcuts are there. And large chunks of my home screens are missing. For example:

Screen 1: Stock calendar widget (4x1) is fine, Internet, Facebook, DC Metro Transit app, and the WiFi switch widget are there, but my GTasks widget and Drive Home shortcut are gone, along with one or two spots I can't remember.
Screen 2: Car Panel, Notes (3rd party), Weather Channel, Brightness widget are fine. But many app folders are missing, including one that held Play Store and Amazon App Store. Pocket Casts 4x1 widget is also missing
Screen 3 used to be the large (4x4) Business calendar widget, but no longer.

Does anyone know what's going on here, and if there's a way to get my home screens and everything back without constructing them again myself?

Thanks.
 
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