Here I go again. After posting my changes to the SWFUpload script I decided I better throw the script up on a server and make sure it really works. Well, it didn't quite work. I've updated the post a bit so hopefully everything is peachy.
I built an ASP.Net demo that shows off my changes. Unfortunately, I don't have anywhere to host it or to post the files for download. So, if you want a copy of the demo files leave contact info in the comments.