[Edi]

Gate Stone, Gift of Kurgi, Soulstone of the Wolves and generally all items that allow you to cast overland rituals: You must have the spell researched as normal before you can use it from the item. This is a known and reported issue.

Units changed by Pebble Skin Suit and Lycanthropos' Amulet retain the magics of their previous form, because the magics are tied to the unique identification number of the unit (which is invisible and distinct from the monster number of the unit). I'm not 100% sure about the Pebble Skin Suit, but the Amulet has been tested. The mage is no use in combat, though, because the Amulet makes him automatically go berserk.

Water breathing items indeed do not affect Air Queens and Cloud Trapezing them into the sea is a very bad idea. See the bug shortlist for details.