So, Northcode is your company?
Yeah, so I'm a little biased

All you should have to do is...

[1] Drag and drop your main movie onto the SWF Studio IDE. It will ask you if you want to make that SWF the new main movie. Click YES. See Building Your First SWF Studio Application (less than 10 mins) for a nice gentle intro.

[2] Drag and drop all your files (or the folder containing them) onto the Files Tab.

[3] Change the Default Base Path on the Movie Tab from "use the folder where the projector is started from" to "use the autoextract folder"

Press the Build button to create a new EXE and give it a try. You shouldn't have to make any scripting changes for just loading SWF files, images, etc. You might have an issue with loading QT movies into an FLV playback component, but if you do I can help you sort that out