IPad 2 Restore - Apps Will NOT Install

Question

I have recently been having intermittent problems with my home button being unresponsive on my iPad 2.  I decided I would try a restore to see if this would resolve the problem.  The home button issue may be better (more time will tell) but whoa did this create an entire new set of challenges.
What I did:
1) Went into iTunes to update all apps afterwards performed multiple syncs and backups just to be safe.
2) After restore to factory settings was completed I attempted to restore iPad 2 to my latest backup from earlier in the morning.
3) Attempted restore multiple times each time an error message states:  The app "x" was not installed on the iPad because the app could not be found
4) The 26 missing Apps appear in iTunes with a "Will Install" button.  Pressing this button changes it to "Install".  Attempted several additional syncs but apps would not appear on iPad.  I also tried to restore with the iPad off, USB disconnected, holding down the home button, attaching the USB Factory Restore to no avail.  All of the missing apps are current and available in iTunes such as:  Amazon, Google, Facebook, LinkedIn, AroundMe, Yelp, Cards, BBC News, etc...you get it...common basic apps all gone missing.
5) Went into iTunes Store on the iPad 2.  Searched in folder for Not on this iPad and Purchased.  Several purchased apps were missing from the list but some were there.  I tried to manually download the apps that were listed from the Cloud as well as manually enter the app name to re-download and install.  All of my missing apps when searched had the Cloud download icon even if they didn't appear in the Not on this iPad or Purchased screens.
6) I am currently attempting to download all the missing apps from the Cloud and will try another sync.
7) What should have been a very short an easy restore has now gone on for over 5 hours as I try multiple syncs, restarts, restores...
Does anyone know what is happening and how to prevent it in the future?
All of my software is up to date.  I am running OS X 10.8.4, iOS 6.1.3, all apps were updated on both device and iTunes library this morning prior to restore. 
My iTunes settings for backups is set to iCloud automotic however I performed a backup to computer before attempting the initial restore.
Please help!
Thanks!!!

Answer 1

I have a similar issue. I recently purchased an iPad Mini, and I started off by backing it up from the apps I had on my iPhone. Now, I have a number of apps that never downloaded and that I don't want on the iPad. Some of these are apps that I don't need, while others are the iPhone versions of apps. There are something like 23 apps that I have no use for, but iTunes tries to install every time I connect. I've also tried clicking the 'Will Install' buttons. There's no way to delete these apps from the iPad without first installing them, as far as I can see, and there's no way to NOT install them, in iTunes.
It''s not just annoying, it's causing problems with installation of larger files and movies. Now, every time I sync to the computer, I get a warning that I'm over capacity by 580 MB, and larger apps will not install! Clicking Revert and a bunch of other things doesn't work, either. And I can't just delete some of the apps, because I or my wife use them on our phones!