I think earth, fire and death sounds nice. Skaven are pretty much into warpstone, warp-fire and stuff that have similarities with banefire and baneblades of dominions. I would probably go for warp-fire national DF spells with decay effects.
Construction of mechanical stuff feels pretty skaven to me. They have warlock-engineers, so acess to mechanical and clockwork horrors seems fitting. Warpstone powered mechanics are quite skavenesque I'd say. Doomwheel is warpstone powered, right?
Clan moulder (is that the name of the mutator clan?) should have B1N1, so they can perform crossbreeding
National 'rat ogre crossbreeding' spell on blood magic seems fitting as well, if you don't want rat ogres as recruitables.
Perhaps Blood to get Vermin Lord as well, unless you make them conjuration or pretenders.
I'm not sure about astral. On the one hand skaven are into Morrsleib (or whatever the warpstone moon is called), and predictions of it's course (That might not have been skaven, but other chaos cults. Can't remember. More than ten years since I played WHFRP). On the other hand they seems more concerned with destroying nature here and now, than looking into the stars.
I think I would go DFEBN. Blood and nature mostly to get crossbreds. Poison is fitting, but can possibly be replaced by more fitting warp poison DF spells that causes decay instead of poison. Similar effect, but not possible to resist with ordinary poison resistance.
BTW nice work, I'm eagerly waiting your final product. I have always liked the WH world. Especially the darker parts of it. Come to think about it, it is a bit dominionesque in being quite close to history. I guess that has unwittingly inspired me in my development of the dominion world.