Having studied the class more closely, I think it's underpowered.
On the plus side, you get a slightly better hit die, and cleric's BAB progression, arcane focus (eschew materials, but 99 times more effective!).
On the minus side is what is supposed to be the Gun Mage's raison d'etre, rune bullets. Why would I focus a 3rd level spell in my gun, just to get an extra 3d6? A fireball's far more effective as a fireball, the same for magic missile. Unless -- and this would make the class worthwhile -- this is in addition to the spell's normal effect. Then we're talking something special.