Samsung Magician migration software is a very good program but it is not flawless (no program is). If you have the time and ability (as in the Windows disk ) a fresh OS install is always best for a new drive.
Try the migration and if you are not satisfied with the result, do a clean install. I have cloned many boot drives and never had a problem, my self. I use Acronis True Image though, which is good software IMO.