All applications were "?" On the dashboard after time machine restore to new hard drive...what went wrong?

Hi folks
I used the cmd R option on booting the MBP and did a disk scan and it reported errors that could not be fixed/repaired.
So I opted to install a brand new 1Tbyte Seagate hybrid hard drive and restore from my time machine backup.
So I installed the new drive in the MBP...it stated that it needed to restore from the internet and I was treated with a rotating globe for about 10 minutes.
It then gave the normal restore options and I opened to format the new drive as a mac drive etc...
Selected the most recent TM backup from USB drive and pointed it to the new formatted HD in the MBP.
So far so good I thought....it said it was restoring....
waited about 4.5 hours and apparently it completed when I was out so I did not see any messages just a normal looking mavericks desktop BUT with "?" In the dashboard where all the applications icons should be?????
I assume something went wrong somewhere so I reinstalled the old HD and restarted TM and it's not starting to backup all 493Gbyte of disk whichI. Understand is normal after a full restore.
So...what to do now??? I'll wait for the 7 odd hours of TM to complete but how best should I proceed with the new HD etc...should I reinstall and copy mavericks to it from a memory stick and then attempt a new restore from the recent TMS backup? Or will this cause issues....
I also have an Inateck hard drive cloning device (brand new never used) so I had wondered if I should simply install the old drive and new drives into this and start the cloning mechanism? OR will this simply clone the errors that were reported on the old drive when it was in the MBP?
In short I'm not sure what to do for the best now and would welcome helpful suggestions as to how to proceed.
thanks
Nick

<<<<UPDATE>>>>
If at first you don't succeed...
Last night after the new 493 Gbyte time machine completed. I once again installed the new drive and restarted the MBP ...waited 10 min for the internet to download the basic disk utilities...restarted the restore from TM and waited 6 hours...Happy days it worked perfectly and like a rocket...the old disk had a read write speed of approx 50-60 Mb/s the new one (hybrid drive) measures at 100-110 Mb/s...programmes open and close noticeably faster and it's better than when the MBP was new...
Apparently this new hybrid drive "learns" frequently used programmes and caches parts that improves start up time etc as time progresses etc...the MBP now starts from cold boot in less than 1 minute compared to 2 plus before...I know minutes should not really matter but it does improve the user experience. I should add I have 16G of RAM installed which does make a difference with Photoshop and Aperture etc.
Hope this helps others or at least encourages people to try hybrid drives over the much more expensive SSD option.

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