When you say you copied all files, had you set up the new drive as either a slave to #1 primary, or as primary on #2 slot?
Normally, it's best to set up the new drive from scratch as #1 primary, partition, format and then install the OS.
Set up the old HDD as either slave to the new drive, or make it the primary on the second slot. Then simply drag and drop all your stuff one drive to the other.
If your new drive goes down, you can soon boot from the old drive (swap leads etc).
Hope this helps.
