I reformatted drive with Time Machine Backups, can I recover them ?

I had an iMac and an External Firewire drive used for Time Machine Backups, All my Personal Files and Music were backed up to the External Drive using Time Machine. The external Drive is a LaCie 500GB Triple Interface Drive. After a few days of upgrading to Leopard on my iMac I noticed that the External Drive was causing some problems, programs were hanging and as a result I had to remove the drive to use my iMac. I later ran Disk Utility to find that there was invalid node struture on the drive. this for some reason could not be repaired.
In between I bought a new Mac Pro and sold my iMac, when I went to transfer everything from the external drive backup from Time Machine I was still having problems so it took me ages but I transferred 11GB of data from the External to another iMac I got a loan from my friend.
I repaired and reformatted the external on my friends iMac not using Leopard and the drive is perfect now, I then transferred the files 11GB back from my friends iMac to the external drive but now all I seem to have is thousands of alias's.
I don't know really how Time Machine stores its backups and this is my own fault for not reading up on it first. Currently I am using Data Rescue II to scan my external drives free space for my deleted files hoping to recover all of them to my new Mac Pro.
Can someone please advise if this will work and if not how can I get my files back. Also is is worth mentioning that when I was having problems with the external drive I noticed that there was something like 250GB Free, and 11GB used not sure where the rest of the 239GB went to? Does Time Machine have files stored invisible or something?

Use migration assistant to move your files.  http://support.apple.com/kb/HT4889

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