I like Eleanor best, and I think both Nora and Nell/Nellie are adorable.
I think I would have trouble counting William as a family name if you sort of think it was grandpa's middle name. That sounds like it's a remote association that other people in your family might not recognize as an attempt to use a family name. It's a perfectly nice name — I just don't think it gets the extra bonus star of "family name" if it's not easily recognizable to you or members of your family.