I don't think that you can do it with IIS 5. (I don't know 6 yet though.)
What you could do is create a file to scan your FTP log files (counting lines would help reduce your load later), use the Windows scheduler to run it every so often, and when you get what you want, run another script to do what you need. Complicated, but...
You could do it in Perl or VB or whatever.
I don't know if you need it to be real time though. The above won't do that. Polling the folder with a compiled application would be more efficient then, but you'd still be stuck with what you mentioned above...
Alternatively, you could have an ASP form to do the upload, and then when it completes, you could fire off what you need to do.