Andy
Not quite clear what the problem here is. I take it you mean that Apple not only put a new OS on your machine, but also removed all of your information, or perhaps installed a new hard drive with that result?
Anyway, if you really mean that all you need to do is obtain SuperDuper and you are a purchaser, that is easy to do. If you still have your registration information, you simply download a new copy from this website and then apply your registration information. If you DON'T still have the info, communicate with
support@shirt-pocket.com and they can help you. Remember too that in the interim you can always download the program and use it in "free" mode until you can retrieve your registration info.
I take it though that there is more to the problem, since you get into bootability of your external drive. Do you need to do a restore of a SuperDuper backup from that external drive? If so, just a copy of the program is not going to help much. The problem is that SD won't let you restore to the volume you are running from, no matter what/where the source of the restore resides.
If you do get ahold of a FW drive AND a copy of SuperDuper, then running SuperDuper from your internal drive you could clone the USB drive to the Firewire drive and be good to go. I may have totally not understood your problem, and if so, I apologize.