I suggest the processor should be in a shielded enclosure. Any digital signals (especially low voltage signals such as crank position sensors) should be carried by shielded wires grounded to the enclosure. Any analog wires (i.e. power supply, analog sensor inputs) coming into the enclosure should be filtered to eliminate noise. The power supply should have overvoltage protection and be tolerant of low input voltages. A buck/boost converter would be a good way to achieve that. You'll need to pay attention to mechanical protection of the board and cables, as well as protecting them against moisture and condensation.