I was careful that I only accepted quests to get the classes I wanted. I had adept as my main class, completed the quest with the candle on the altar, and completed the charging of the crystal, but when I'd talked to the priest it skipped the dialogue of him telling me I'd been promoted and went right into telling me about the clarity crystals quest.
I made another Thrall who was nearly identical besides a couple different heraldry, and this time I was able to successfully unlock the class. The only difference this play through was that I didn't get the moonstone and lock myself out of Fargrove, as I was afraid that maybe I'd needed to go back to the priest there to complete it, which wasn't the case.
I assume it was some kind of bug that caused this. At least the second time I had a better idea of what to do so it didn't take me too long to take another shot at it.
Anyway, thank you for the quick responses, it can be a real pain trying to find solutions for older and less popular games sometimes.