Engine Misfire & Rough Idle: Troubleshooting

I don't want to bother the respected community, but I'm having major problems with my car.
Problem description.
'The engine jerks in every gear at an RPM of 1200-2500 during normal acceleration. If I press the accelerator pedal fully and shift to 3500 RPM, the jerking is not noticeable. It also doesn't produce any smoke. I have already replaced the mass airflow sensor (MAF) and the diesel filter, but without success. The injector spray pattern is fine, and the knock sensor test was performed without any issues. When I disconnect the knock sensor connector, the jerking is still present, but significantly reduced. I scanned the error memory with VAG.COM, but there are no error codes. When I clear the error memory with VAG.COM, the jerking is reduced, but after 50 km, it returns to its original state.'
The engine runs roughly, and everything seems okay after starting. However, if you shake the car, the rough running immediately starts. Repeatedly pressing the accelerator pedal will then restore the idle speed. This also happens when you're driving off the highway and have to stop at the next traffic light. The rough running sounds like an old tractor (WUP WUP WUP).
The car is a 1994 Volkswagen Golf 3 TDI 1Z with an odometer reading of 140,000 kilometers.
As you may have noticed, I am a beginner, but I ask you, those who are more knowledgeable, to help me, the ignorant.
Thank you.

Just search for 'ruckel' and '1z'; you'll find everything you need to know!