Properly decouple Arduino in and output with opto coupler from engine noise

I think the 1µF is marginal for really fast spikes, but it might be OK since this a motorcycle.

What capacity would be a appropriate?

If this were a vehicle I would vehemently disagree with you on this point. However for a Motorcycle, I don't have any experience.

I have never connected an oscilloscope, I have only a fixed installed voltmeter, so you are probably right. Is the source of the spikes the ignition system? Then there should not be a difference between a car and a motorcycle. I can connect tomorrow my DSO150 to check it.