The issue was something with the BDC taym was right. I fixed it with EasyBCD http://neosmart.net/dl.php?id=1 .

I'm not exactly sure how I did it I think I removed the BCD then made a new one on the right drive. Then when I re-booted the computer wouldn't boot unless I disconnected the old drive.

So then I connected both drives with the SSD connected to port 0, booted from the windows disk and let it fix whatever it decided was wrong.

After that the old drive no longer shows being a system drive so I was able to create a backup using the windows utility.

Not sure if this was the best way to do it I will find out when I try to restore from it someday.

Thanks !