There's more than one poster in this thread with a misfire problem and a solution for one isn't necessarily a solution for all. A misfire can be on one, 2 or all cylinders and the faults could be different. I suggested you had to eliminate these first with simple swaps before removing and replacing parts without confirmation they were actually faulty.
You can't eliminate the ECU for some misfire faults. When the ECU mosfets are driving the ignition coils at higher rpm, misfiring can be caused by lack of speed and one culprit is when people put in aftermarket coil packs. The ECU coil triggering at high rpm is matched to coil pack inductance and resistance to get the fastest and most reliable spark triggering. OEM coils are designed for consistent operation matched to the ECU mosfet drivers. Chinese equivalents and so called booster coil packs may not be.
Testing for sync between fuel injection and ignition timing is a bit harder to do but eliminates important variables, leaving air mixture as a possible fault to follow. Since it's an Efi engine, the flap valve is in a loop with control inputs coming from other parts of the system - e.g MAF and temperature sensors.
The way to check and eliminate any misfiring due to missing injection or ignition timing pulses is to use a 20mHz dual channel USB storage scope on a laptop. You put the injector pulses on A channel and use the B channel to monitor HV spikes from the coil pack. Run the motor at idle when the fault is ocurring whilst capturing the pulses. There should be no timing gaps and an ignition pulse always occurs after an injection pulse. On these engines there are TWO injection pulses and one ignition firing pulse per cycle. Play back the captured sequence and check the injector is always fired twice later, again with no time gaps compared to the previous pulse triple
Maybe you aren't up for this and you will just go straight to replacing the flap valve assembly? When you talk about the stratify position I doubt it will be one position, but a variable position determined by other sensors, e.g the ECU fuelling map, temperature sensors and DI fuel pump injection pressure control? When V.W design these closed loop Efi feedback control systems, they often build in preset limits to ensure the engine will keep running of sorts, even if there's a control loop problem or a critical sensor is working outside its expected range. If I saw the flap valve moving to different positions as sensors warmed up I'd think the feedback loop was in control. If the flap stayed in the same place each time at cold key on, even after fooling a temperature sensor, I'd think the control loop wasn't working?
You can follow the attached links which explain how extra fuel is injected twice and on the compression stroke just before ignition. This will be the highest compression point where the DI fuel pump must produce a greater pressure. This suggests these injectors may be a special design? I assume all these important parts are genuine OE and not substitutes? You said it would be hard to swap an injector so it still remains an uncertain item? On my Tdi I unlock each injector fuel union, fiddle them out around the steel fuel lines or remove the lines for better access, then bleed fuel through after replacing.
Let us know what you are going to do next.
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