Klaus is correct, I should have added a series resistor before the capacitor. For your situation a 10K in series with the input and just the capacitor on the output. Calculating the RC is probably not too helpful since you don't know exactly what you are trying to filter.
Another good design option is to keep all the wires coming to and from the Arduino (including the power) kept in one bunch. And all the grounds common.
Now the opto's. In an automobile the "ground" (should be common) can vary 2 volts from the battery negative. Although there are other ways to accommodate this variation an opto could be useful. I can't imagine in a motorcycle such a large variation exists.