Okay, i found this:
http://bytescout.com/swfscout_flash_demo_exe_to_swf.html[
^]
Which is taking the swf out of the exe, it also comes with source. I'm not sure what language it is since i didn't look but...
Anyway, if you know how to take the SWF out, then that means you know where to put the SWF back in. So you may be able to figure it out from this.
Remember, if you get stuck with a specific problem then feel free to ask away.