Protection against back EMF
Electrical noise on vehicles (auto or motorcycle) is atrocious. There are a few things you can do to mitigate this. 

Hard pull ups or pull downs. If you were going to use a 10k pull up, instead use a 5k or 1k. Be sure to keep in mind the drive capability of anything on these line so you don't burn something up. 

Isolate your circuit from everything. Use an isolated buck converter. Use opto-isolators on the output. Keep the noise from getting in. 

Decouple everything. Add capacitors every were. Use capacitors to form low pass filters on inputs. 

Debounce the button in software. Don't just read the button once and assume it's high or low. Read the button once a millisecond. If the button has stayed at a steady state for more than 50mS then change states. 

Use a metal enclosure.