Haven't played in awhile, but this sounds really impressive reworking!
One thing I thought of that you could add, is upon new game+ ing, to allow the toggling on and off of the bonuses the achievements grant you. These choices would be permanent for the current playthrough. I only suggest this because too many of the bonuses make things too easy currently, may grant bonuses to undesired stats, or to allow for players to challenge themselves. The achievements story wise could still be considered active, only the stat buffs are not granted.