What you should really is find an external kit that you can put your old/new drive into. Then you could first put the new drive into that case and then clone to that drive. Then take that drive out and then remove the old hard drive from your Mac. Now put that new drive that you cloned to and put that in your Mac. Now you can boot from that drive.
Then you are almost done. Now put that old drive into the case and mount it on your Mac's OS X system and then boot from that external. This was once you are booted from the old drive you can launch Disk Utility and you can use that to repair permissions on the new internal drive.
Lastly you boot back into the Mac's new internal and then erase your old drive or keep it as an emergency bootable backup. Just remember to keep the external drive updated.
See what you can do in OS X, booting from externals can be VERY beneficial!