I've had problems with misfires on my 2012 Fabia for a long time now, but it's been too subtle to notice while driving, and only really shows up on my scanner.

This summer I changed my timing chain to the upgraded version and cleaned the intake valves. The spark plugs, coil and wires as well as a leaky Non-Return Valve have also been changed withing the last 12 months without improvement.

I did a drive while recording the misfires and what situation they occurred in and found that all cylinders get misfires (between 1-3 each in 15 minutes of driving). I got 2 misfires while idling, 1 while driving normally, and 2 on the same cylinder right after putting it in "Sports" mode and giving it some gas. My total misfires are up to between 4k and 10k on each cylinder within the lifetime of the car, so I think this has been happening since I bought the car 4 years ago.

There is also a rhythmic hesitation or hiccup that occurs especially when the engine is cold, but gets more subtle when the car is warm.

The next thing on my list of things to try is to change is the vacuum hose (03F 133 751 B), but this is quite expensive, especially when I don't know if it's the issue or not.

I can't quite figure out what is causing this problem and would appreciate any help and ideas :)

Try some Forte petrol injector cleaner! Injectors can tarnish and affect the spray pattern.

You have done coils and plugs.