Ghouls are supposed to be the game over enemies for majority of the game. Player should only be in the caves for a short amount of time and when you hear the growl, you know it's time to leave quickly. Noclip is a workaround, because the engine has no pathfinding and this is a simple temporary fix. Ghouls will be worked on more in the future. One simple solution to make them slighly easier to deal with is to make them glow a little in the dark, so you can see them coming.
Animal killing no longer affects the mood loss. Morality now does. Once your morality goes to -10, you should stop getting mood penalties for killing animals. Morality can be lowered by killing humanoids or animals.
I checked and I don't see any reason why great coordination should affect wellness. Is there something else you did before you noticed the wellness increase? Joining the church increases wellness for example.