Im only cheated to get item like, strong health potion and strong mana potion or anything related to potion, and for spell i just do it until i cant learn anymore spell until i level up. And i cheated like level just to fight the elves and the level back to normal again not stuck at max level. So is that cheating item, and level make different in the play through or not?Probably you are still missing a step.
I've seen people get locked in this game because they cheated and by doing that bypassed certain steps (such as learning spells when they became available) the game expected to be completed, or skipped time in-game by cheating.
Also, out-dated mods can break the game.
Can't tell if anything of the above is applicable to your case of course.