Are you actually sensing RPM from the spark source in your project (not sure if your posted project schematic is all of it or just some of it) ?
If so I might be able to help suggest some things. If not, then I'd suggest you try initially powering the project from an independent battery source (dry cells etc) and see if your problems go away. If so it gives a clear indication of whether the source of EMI (if that's the issue) is coming in via the cars own power supply.
Also be aware that any long sensor pickup lines in the car are potential receiving antennas for EMI, and use inline RF chokes before they get too close to the MCU.