Help getting data from iTunes onto my New iPad from iPhone backup

Hi for 2 days now I have been trying to sync my New iPad2 with my iPhone 3GS, I have followed lots of threads & advice which has been helpful but its not quite happening for me!
I set up iCloud and iTunes as advised, my iPhone & iPad share the same Apple ID. I backed up my iPhone to iTunes successfully, and restored the iPad via iTunes using the iPhone backup, it went thru the motions OK so I assume completed but I can't see any change.
Under "Purchases" in my iTunes account it has two tabs one for the iPhone and the other iPad listing all my Apps so clearly it recognises my Apps but the Apps only feature on my iPhone I can't get them onto my iPad. I even deleted some apps and reloaded them since the sync & backups but it still doesn't work. Strangely under my "Account" in iTunes it says only 1 Device is recognosed by iTunes and thats my New iPad, yet it still shows a Tab under Purchases for my iPhone so I don't understand why this is not listed as a recognised Device under the Accounts tab.
My contacts, calendars etc are in sync between the two devices wihtout any trouble at all.
I did think it was because some of the apps were downloaded before the sync / backup but some threads lead me to beleive you can sync the content no matter when it was purchased. Under the "Purchases" tab for my iPad I can view my "Apps" which has a "Download all" option so Ibeing at a loss what to do next I proceeded to Download All and it was clearly doing this for some time but still nothing on my iPad.
I was advised to turn iCloud off whilst I do the backup and restore on iTunes, and then turn it back on after. I have turned my iPad off/on after these updates but still the apps do not transfer across.
I feel like I am so close now but for some reason something is still not working! Please Help - thankyou.
(Just to add both devices are using the latest software update & iTunes working with Vista Windows on PC.)

Connect and select iPhone in computer iTunes sidebar, in Music tab,
select
     Sync Music,
     Selected Playlists, artists, albums....
     Select the music you want on iPhone.
     Click Sync button (bottom right)
Here's the iPhone user manual
iPhone User Guide (For iOS 6.1 Software)
Message was edited by: ckuan

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