The Bavarian village will really be fun to create.
I made a 4-way crossover with FasTrack and play timing games with two trains changing lines. Much like real railroading, slow speed when switching is much safer. 
Don't ask how I know.
The 3D objects helps to confirm any scenery ideas that you have in deciding if it will look ok or not.
It appears that you are close to your original ideas.
I have always liked the "pretty blue light" of Cherenkov radiation. Perhaps you can put some blue leds in your waste building, as if the storage pool was getting a little hot. Fukushima is still making pretty blue lights, but we don't hear of it any longer.
Have you considered the #452 Nuclear reactor and some AEC cars to perhaps stay with a fantasy theme?
