Thanks...

I ended up running the mpeg through FlaskMpeg to get an uncompressed avi(no audio) to take into Sorenson Spark Pro (demo version). Then I took the flv out of sorenson and put the seperated audio file on another layer set to stream. It works very well and cut the file size from 555k to 265k.

I had some issues with the wildform program, Flix. I couldn't control the output well enough to get what I wanted. The file size actually increased and it dropped frames like crazy...I think its more of me not knowing how to use the program.