I downloaded Ziltoid via torrent shortly after it came out.

I finally bought the special edition, and now I have a question.

On the copy I downloaded, at the end of "Solar Winds", it says "Fooey, indeed, fooey"

On the special edition, it says "Fooey, and double fooey".

Are there any other changes?

I don't think that's a difference between the standard and special edition, but rather a difference between the promo (which the download is) and the purchased version.

...And that's the only difference I am aware of.