Spark plug cable firing interrupts
Without knowing the type of .1uF capacitor you are using in the low pass filter, I would suggest adding a lower value ceramic cap in parallel with the .1uF cap, similar to the 100nF cap that is in parallel with the 1uF cap on your Vcc bypass. 

The noise from the spark is wideband, extending into RF. Capacitors have parasitic series inductance that becomes important at high frequencies. Most capacitors will typically act as inductors at a high enough frequency, and the transition typically occurs at higher frequencies for smaller, lower value capacitors. Parasitics vary widely depending upon the capacitor construction.If you click on a capacitor type at this link, you will be able to select parts, compare their frequency response and download their spice models.Kemet has a tool for modeling their capacitors