Earlier this summer, I worked on the BPJ engine in my Audi A6, cleaning the intake manifold and intake valves. I also replaced several gaskets, high-pressure fuel pump's cam follower, and I also did timing belt and auxiliary belt, spark plugs, PCV valve and its hoses. In hindsight, I should have done these steps a bit more gradually and test someway in between.
Anyways completing all that now I'm experiencing a recurring misfire in cylinder 3 (error code P0303), with no issues in the other cylinders. When starting the engine cold, everything is fine while the RPMs are higher, around 1200. The problem begins when the RPMs drop below 800. The engine sound becomes rough, it starts shaking, and the misfire count begins to rise. When I increase the RPMs to around 900-1600, the misfires stop, but they occur again between 1800-2600 RPM, and then disappear above 2800 RPM. When testing at these RPM ranges, the engine also smoked a bit from the exhaust after warming up. I also tested for vacuum leaks using smoke around the throttle body but couldn't detect any leaks from the intake manifold or the breather. I also disconnected the MAF sensor, but it didn't change the how it runs.
I tried swapping the positions of spark plugs and ignition coils, but the misfire didn't follow with them. One difference I noticed related to cylinder 3 is that, when looking into the spark plug holes, the piston in cylinder 3 seems shinier compared to the others, which are more matte. Using a cheap endoscope attached to my phone, I tried inspecting the cylinders, and they all seem to have similar carbon deposits, though cylinder 3 might have slightly more brownish coloration (possibly oil?). When I recall removing the old plugs, cylinder 3's ignition coil had some surface rust, which I cleaned off. I can't remember the condition of the old plugs from each cylinder, but there might have been a bit of oil on one of them. The new plugs I've used during testing mostly look similar, though cylinder 3 might darken slightly more. I recently measured the compression pressures, , cylinders 1 and 2 were at 198.5 psi, cylinder 3 at 196, and cylinder 4 at 196.5, so no significant differences there.
Do you have any tips on what I should try or check next? What I've been thinking is that one possibility could be a faulty or clogged injector now. However I'm hesitant to remove again the intake manifold etc. unless it's absolutely needed (one stud's threads not the in the best possible condition anymore).
Is there any way to confirm that there's something going on with the injectors without removing them? I've understood with a VCDS some values could be read on individual injectors, however I don't have one.
Also I ponder what to determine about the different apperanece of the cylinder 3?
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