A discolored quilt top should be quilted and bound first, before washing. If it's just stains, they should all come out by using
http://www.retroclean.com on the finished quilt. Some of the stains from storage in cedar chests do not come out because these are caused by acid eating into the fabric. All wood products (including paper, tissue paper, cardboard) contain acid unless treated to be acid-free. However, it sounds as if this is not the case with your inherited tops.
The blue markings for the cross-stitch may or may not come out. In any case, I would still make those up into quilts. IMO, if the blue marks don't come out they simply add to the vintage appeal of the quilts. Plus, quilts are loved even when they are not perfect (which is the case with most quilts).