Finally, 4 years later, I solved this problem.
As the car is an auto to manual swap, my new configuration was still based on a .bin for an automatic transmission car. I used all tables from a .bin for a manual car and deactivated the automatic transmission.
After the new VSS sensor didn't work either, I flashed an unmodified bin from a manual car, and boom, it worked!
Obviously there are some important bytes in the "unknown values" region that are needed to get the VSS input working properly!

So you always need a manual .bin for transmission swaps, not just change the speedo scalars!

I'm just still trying to find out why the speed on the speedo and on the loggs are different. At 100 kph speedo, my log says 73kph...