Running it tomorrow. I still have no idea how Thrune's to be scaled for 4PCs, so I'm going to simply disable his artifacts, considering they're in dormancy for some reason, giving him the spear as a plain magical spear.
Also, I'm not convinced by some GMs' use of plane shift as an offensive spell. I know it's legit (though I'm really not sure it was originally planed to be used that way in 3.5), but I question whether the creature would use it, knowing it has to support Thrune and Lissala in the future (not to mention being offensively plane-shifted itself). That's the same issue there is with the limited wish(es): it was specifically told to keep them to assist Thrune, so... that would be a last-ditch spell.