You may be overcomplicating what needs to be done. You should be able to incorporate the calculation into your Flash movie and display the result right in the same movie.
If your shipping calculation engine was/is an existing perl or PHP script, then you could call out to that script and then have it send back the result to your movie.
I don't have control over the SWF..
Think of it as Wholesale pricing that I need to markup and display my own pricing to my customers.
So I want to pull that pricing data, manipulate it (adding my markup value), and serving my new numbers to a front-end website.
Depending on what the data looks like coming from the Flash movie, you can use the get or send method to output data from the Flash movie using URLRequest. You can look at the online help example for the URLVariables class. You will still need to use or create a server side script to read in the data, make the changes and send the modified data back. That will be a perl or PHP script and is outside the scope of this forum.