You must be editing the wrong file, the site uses skins from /Data/Sites/[SiteID]/skins not from /Data/Skins, so in most cases it will be under /Data/Sites/1/skins/[skinname]
Myself I don't like the way that toolkit works and requires extra elements. Even if you change to xhtml doctype and add those declarations it may be technically valid, but it will not pass the w3c validator.
Hope it helps,
Joe