I already tried the nozzle cleaning the way you described, I let a piece of PLA smelt in the extruder and pulled it out at 80 deg which helped me pull out all of the inside plastic in the extruder. I got a perfect shaped extruder inside form, even with a small top piece of .4mm so I'm sure it's clean..
I've only used PLA on this printer from ultimaker which is approx. 2.85mm.
I did the pulling force test and the machine skipped steps at 2KG and later at 3KG.
It feels like the extruder motor has not enough current and the heated block is just not heating the filament quickly enough..
It's very likely not the extruder in my opinion. Even though the nozzle is "clean" there is probably some ABS or other gunk stuck to the inside wall. To prove whether the problem is the extruder or not you can do this test:
Is it possible that the filament is more than 2.99mm? Once filament hits about 3.00mm it tends to not be able to pass through the bowden.
To clean your nozzle more thoroughly I recommend getting some metal that can fit in the nozzle such as hypodermic or acupuncture needle and doing this:
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