TLDR: The motor was faulty, and it was replaced
I’m not an expert on electrical motors, and obviously without ”autopsy” we can only guess what went wrong in the motor. Besides being noisy when rotated (the 2 other motors present didnt make any sound), and also the FFb being mushy across the board, which became evident after trying a new motor. Unfortunately, I have to say that the notching is inherit to these motors (at least both other motors notched when rotating without power), but at the same time notching was way more tolerable with the new motor when driving vs the old one. And in roofed cars, the notching was practically absent with the new motor.
When I first got this system late last year, I quickly realized that I need to use max reconstruction filter with it, since otherwise it would give these very hard spikes here and there, around a lap of any circuit and with any car. With the new motor, I can lower the reconstruction filter to lowest, and the torque bandwith limit to unlimited, and still dont get these hard spikes like I had with the old motor. Driving with the new motor, the FFb was way more clear, even with the same settings of max reconstruction filter that I used before. We also replaced the cables, altough it didnt noticeably change anything. One more side note, the first thing I realized after setting the new motor up at home, was that before I got noise from my old Logitech 5.1 speakers when the Simucube was powered on (before I needed to turn the sperakers off to avoid this), and now with the new motor (and cables), it doesnt happen anymore.
Lastly I would like to say huge thank you to Simgear (Finnish), for being very patient and helpful with this problem. In the future I’m not afraid to buy even the most expensive stuff from there, because of this kind of outstanding customer service. Keep up the great work!