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Whilst saving what I wanted to keep and put on to my new pc by transferring photo's, music, documents, favourites, passwords to an external HDD. I also used 'Windows Easy Transfer' program (it comes with W7) and put a copy of that on to the external HDD.
When I got the new pc up and running I used the 'Windows Easy Transfer' and lo' and behold everything was transferred including favourites and passwords, without touching my exported favourites and passwords files. It took a while to go through probably because the file was 60Gb in size.
Chucks answer was the best answer to my question, but 'Windows Easy Transfer' can do it as well.