I had what I thought was the same issue, but I WAITED FOR ABOUT 20 MINUTES AT 99%, AND THE PROCESS COMPLETED ON ITS OWN!! The Magician software is probably not hung (or stuck). My cloning of a .5 TB to a 2.0 TB disk took about 4 hours, and was seemingly stuck at 99% for about 30 minutes before COMPLETING and displaying 100%, and "migration complete".
And the clone was installed and successfully booted as expected.
So, folks, the solution, as with many things, is to BE PATIENT. Just let it run.
I hope this helps. Because I did not see this solution anywhere else.