Filtering 5V and 12V in a noisy automotive environment

With a wire of any length, I would install .01uF caps at each end and maybe in the middle too to bypass RF to ground. I would also install a 5.1V Zener or transorb on the wire to keep spikes out of the micro. The cleanest power in the car is at available at the battery terminals. The battery is effectively a giant capacitor. To get the cleanest power back to an accessory, tap off of both terminals and don't use the body ground. Fuse both wires near the battery.