I think Whink might damage the fabric.
I would use RetroClean (
http://www.retroclean.com ). However, if you are thinking of removing the spots before the top is quilted, you would really need to baste it to a foundation fabric for stabiity first.
By "rust stains", do you mean the stains were actually caused by rusting metal? Or that they are just stains of unknown origin that look like rust? I think the word "rust" may be misleading.