Flitz is good, and if you scan the shelves at your marine supply store you will find a variety of mild polishes designed to clean clear canvas.
This hit me after dinner tonight and I had to get back to you.
You say "rust stains" on your clear canvas. Ok--but often brown "staining" of clear curtains isnt stain--its heat damage from the panel being in contact with the piping for your top. If that's the case, you may have irreparable damage. Sorry to bear this news and hope that's not the case.
FYI--better canvas enclosures usually have solid materail strips where the "windows" touch the pipework. Or, they are tailored so that the fabric doesnt touch the pipes at all.