What's the hold-up?
 

I've used SuperDuper successfully for several years and love it. I'm running 2.5 (v84).

As I write the "Repairing permissions" step [Smart Update] is at 40 minutes and counting. I've never know it to take anywhere close to this long. Any ideas as to the source of this problem?

Sure: "Leopard". :)

I'd turn that option off.