Great tip on the swfObject code! I've achieved the desired results by "composing a webpage" in moodle and using the HTML code generator to embed the swf file.
A tip to anyone else who tries this: the HTML code generator outputs the HTML for an entire HTML page. If you cut and past the whole thing into the HTML editor in moodle, the swf won't appear. However, if you go back and "update this resource" and inspect the HTML code again in the editor, it will have stripped out the extra code, and the second time it will appear properly.
Next I want to take Matt's suggestion to look into AIR. I hear it's great but I don't know anything about it. Any suggestions on where to begin?
General plugins
Flash module add-on: Size of Embedded Flash
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