Some progress today. The pump trick didn't reveal any obvious air ingress, so I concluded air must have been coming in from the filter or from any of the hoses plugged to it. After taking it out and re-sealing all connections, plus adding a manual pump between the filter and the IP, bubbles are gone.
I wouldn't say the engine runs smooth though (although it runs better). See this new video I made with the engine already warm:
https://www.youtube.com/watch?v=5sj0Qs2NnIA. If you wait till the end, you can see that giving gas leads to increasing amounts of black smoke (unburnt fuel?). I guess it'e either running too rich or there's still something wrong with injectors.
When idling, it also runs pretty uneven - although much better than when air was getting in. See this other video where this is more apparent:
https://www.youtube.com/watch?v=H8iyOsAbij8
What are your thoughts?
PS: In other news, I managed to strip one of the head bolts when giving them the last 90 degree torque (the one that you are supposed to do after warming up the engine to 50 degree celsius)
.. I was able to hammer the tip I'm using into the stripped bolt and left it like that. I will order a new bolt and replace the stripped one, hoping it will come off.. so until then, no more fiddling around I'm afraid.