You only need to seal the body prior to grain filler if you are using tinted filler. Otherwise, as you found out, it also stains the wood.
Some more info http://www.reranch.com/101a.htm
You should be able to remove the black by bleaching with household bleach and hydrogen peroxide if it's a dye based stain. If that doesnt work you can use swimming pool bleach which is much stronger.