Q: Nissan Xterra shaking stuttering and check engine light

The flashing check engine light is likely due to misfiring. If the engine is misfiring that can damage the catalytic converter. Try not to drive the car until it is repaired. Inasmuch as ignition components were removed, my guess would be the misfiring is due to a poor or broken electrical connection. Spark plug wires, in particular, can develop breaks if mishandled or simply due to age. A possibility is download the trouble code(s). If, by chance, the code(s) implicate misfiring in specific cylinder(s), use an ohmmeter to measure the resistance in the spark plug wire to that cylinder. If you get an out of range (out of spec) reading, replace all the spark plug wires. Use name brand wires such as Denso, AC Delco, or dealer supplied. If that initial check of the codes does not yield an obvious explanation of the misfiring, due to say spark plug wires, if you request a Check Engine Light diagnostic the responding certified mechanic will promptly diagnose the problem and get your car running properly. If you have further questions or concerns, do not hesitate to re-contact YourMechanic as we are always here to help you.