Have a look at diy-efi.org. There is a link to a site that has circuit diagrams for the Delco fuel injection computers. See how they cope with this problem. Whenever you have real world inputs or outputs, you must protect them against expected worst case voltage inputs,spike and pulses. As well as some filtering and protection your software needs to debounce the inputs so that it doesn't respond to a spike on the input. If the inputs are slow like a switch, you might have the software check to see if the input is active for 100mS before acting on it.

You will see that in the fuel injection boxes that most of the components are for protection - for good reason. Think very carefully about failure modes - what happens if an input fails? What will your box do and how will you alert the user that there is a failure? What diagnostics have you built in? Most fuel injection boxes flash a code sequence on a led or dash mounted lamp. Most of these features add little in the unit cost but make your unit more robust and reliable.