Had my mechanic go over the car again to see if something comes up. Nothing did and he said it seems like the last issue is software related since everything else checks out and only the dealership is able to do that.
Went to the dealership and agreed that they will do a full on "investigation" part by part, step by step. Gave them a list of everything that's been done to the car, like in this thread and they began work.
3h of work later, I get told that they have no results after trying various things and want some 3 more hours, yet they ask £130 for an hours work. I'm already at £390 and they want another £390 with the possibility and no guarantees of finding the issue with.
In the 3 hours, they removed my exhaust, checked EGR, checked timings and replaced the tensioner as well are reprogrammed the injectors just in case electronically there's something wrong. No change.
Next they want to check every single injectors
(even when all but 1 of them work just fine) and want to check the swirl valves. I would likely go ahead with this except for the £130 an hour asking price. I'm looking at another £600 with no guarantee for a fix, so I guess it's time to save up again. A Scania dealership asks only £70 an hour. Don't understand where this £130 comes from.
In the meantime, I've taken the car home and maybe I'll takle this myself while saving up. I guess it's time for me to become an expert on D5 engines
Glad to know at least that the EGR valves, DPF filter, its sensors and timing are not to blame as they're working fine. Not everything's a waste.
Really excited forwards to what will happen in the next few months.