Apps are not being transferred after updating to new iOS

I've read a few posts but nothing explicitly about this issue. I am the original account owner, same computer, iPod has worked with the same apps for over a year until I updated to the new iOS a few days ago.
I recently updated my iPod Touch to the new iOS a few days ago; it transferred all my music, and everything else, except for my apps. I tried Store > Authorize this Computer on my desktop (which reminded me I'm still authorized, oh joy) as well as Settings > Store on my iPod. I'm not sure what I need to do next? Any suggestions would be greatly beneficial! Thanks!

Before I updated to iOS 5.0.1, I was given 3 options "Download and Update", "Download", "Cancel" (or whatever). I chose to just download, without installing it, which would allow me to back-up all the data from my iPod to my desktop. I presume that path wasn't available if someone selected "Download and Update" immediately which informed me that it would erase all data without actually backing up before it installed. I'd have to assume at that point when your apps were re-installed after your update, it would still keep the previously saved sync data from the last time you plugged into your computer. I'm not sure if that was the case for you, but I never signed in to Game Center until now so I'm not sure how that works. This is also considering that iCloud was just introduced to mobile devices. Hope this helps :S, if not good luck! Cheers.

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Try resetting the SMC and pram
To reset the SMC
Shut down the computer.
Unplug the computer's power cord.
Wait fifteen seconds.
Attach the computer's power cord.
Wait five seconds, then press the power button to turn on the computer.
To reset PRAM/NVRAM
Shut down the computer.
Locate the following keys on the keyboard: Command, Option, P, and R. You will need to hold these keys down simultaneously in step 4.
Turn on the computer.
Press and hold the Command-Option-P-R keys. You must press this key combination before the gray screen appears.
Hold the keys down until the computer restarts and you hear the startup sound for the second time.
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I tap iPhoto and it tells me to marge the photos to Photos app. It was going fine and then suddenly, it closed. Now i can't open the Photos app anymore. I've rebooted and deleted iPhoto app. I can't even open through Camera.
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Must be serious because you have stated the problem 4 times now.
Here are a number of things that you can try and maybe one of them will help.
Reboot the iPad by holding down on the sleep and home buttons at the same time for about 10-15 seconds until the Apple Logo appears - ignore the red slider - let go of the buttons.
Make sure that you do not have a stalled download in iTunes - a song or podcast .... if you have a download in there that did not finish, complete that one first. Only one thing can download at a time on the iPad so that could be what is causing the problem.
If that doesn't work - sign out of your account, restart the iPad and then sign in again.
Settings>iTunes & App Store>Apple ID. Tap your ID and sign out. Restart the iPad by holding down on the sleep button until the red slider appears and then slide to shut off. To power up hold the sleep button until the Apple logo appears and let go of the button.
Go back to Settings>iTunes & App Store>Sign in and then try to update again. Tap one waiting icon only if necessary to start the download stream.
You can also try deleting the waiting icons - tap and hold down on an icon until it wiggles - the tap the X on the icon to delete it. Then try to download again.
You can try resetting all settings. Settings>General>Reset>Reset All Settings. You will have to enter all of your app preferences and device settings again.
You can also try going to the App Store, find an app that needs an update, tap on the app icon to bring up the description page, then tap on install that way, rather than using the Update option from the app updates screen.
And ... You can always install the updates in iTunes on your computer and then sync them to the iPad.

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Problem:
When I plug in my iPhone to sync, it starts but does not complete the process and several pieces of data are not being transferred to my iPhone from my MacBook Air.
Any help that you can provide in helping my iPhone accurately sync with iPhoto and iTunes will be greatly appreciated.
Symptoms:
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waiting for sync to start (step 1 of 7)
backing up (step 2 of 7)
preparing to sync (step 3 of 7)
determining apps to sync (step 4 of 7)
preparing apps to sync (step 5 of 7)
importing photos (step 6 of 7)
waiting for changes to be applied (step 7 of 7)
syncing apps / copying 1 of 4 (App name) (step 7 of 7)
canceling sync
apple icon
2)   Photos: I've selected only certain of my iPhoto albums to sync to my iPhone. All of the albums are correct/complete in iPhoto. All of the albums are listed on my iPhone, both before and after the sync, but the albums are empty (no actual photos) before and after the sync. Perhaps this is tied to the fact that the sync isn’t completing, but because “importing photos” is one of the steps that the incomplete sync displays, I don’t know.
3)   Apps: When I launch iTunes and click on the Apps folder under the Library listing, then click on the Updates tab, iTunes searches for any Apps needing to be updated and provides a list. If I click on Update All, the Apps are successfully updated in iTunes. But, when I plug in my iPhone so that the updates will transfer to the apps on my iPhone, the updates don’t transfer to the apps on my iPhone and those apps still reflect that they need updating on the iPhone.
Other Potential Pertinent Info:
The flash memory hard drive on my MacBook Air recently died (perhaps a month or two ago). Apple had emailed me about a known issue and literally the next day, my MacBook Air crashed. I installed a new flash memory drive and re-installed everything from a backup off of an external hard drive. Everything seems to be working fine; it recreated accurately all of my software and data, including iPhoto and iTunes, the pictures and songs (respectively) for which are stored on that hard drive, as opposed to being on the flash memory in the MacBook Air itself. However, I don’t recall if the start of the sync problem described herein started happening at the same time that I replaced the flash memory drive. All I know is that the computer is working perfectly in all respects and that even as the sync is failing, it at least says that it’s doing the right things and looking in the right places (e.g., the list of albums on my iPhone matches the list of albums in iTunes, etc.).
Settings/Status:
MacBook Air
OSX v. 10.9
iPhoto ’11 v. 9.5 (902.7)
iPhone iOS 7.0.4
iTunes v. 11.1.3 (8)
Summary Tab
Backups (This Computer)
Options
Automatically sync when this iPhone is connected
Sync only checked songs and videos
Photos Tab
Sync Photos from iPhoto (429 Photos)
Selected albums, Events, and Faces, and automatically include (no Events)
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http://support.apple.com/kb/HT4137
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Apps are not being transferred after updating to new iOS

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