That is a cool house! I assume there might be some issues with the rock wall. Such as water infiltration. If you like it and want to keep the rock wall I would celebrate it! Meaning leave it as is and add some accent lighting to highlight.

The item that bothers me in the pictures is the railing on the stairs. This is a very traditional (a little outdated) railing. I could see a rustic or modern railing depending on your style.

Personally I like modern and would try to find a railing that blended in (ex. cable rail) and made it look like the only structure there was the rock wall and the stair treads and stringer.

Good Luck!