So I did what I should have done from the start and opened up the new Macbook Pro again, took the drive out and put it into an enclosure, I then used SuperDuper! to clone the drive from the old MBP to the new drive in the enclosure. The whole process took around 3 hours for 170GB.
I then put the drive back into the new MBP and booted up, boot was a little slow the first time but since then its been working perfectly.
The problem was that I was trying to make my life easier, having a baby in the house and so as a result not having as much time to focus on the computer as before, I decided it would be faster and easier to mount the new drive into the new MBP, which obviously wasnt the case - I guess for me the moral of the story is to stop and think a bit more next time, which if I had, would have made me realise that the enclosure was the way to go from the start.