It was weird and I was quite surprised that I had the codes. I was very careful not to disturb the angle sensor while I did the install and everything went very smoothly. Thats why I posted my findings to let those know that even if you do everything correctly there is still a chance the car wont be happy. Also just for info, my e90 is a 6mt, no idrive and the fault codes did not appear till after 30 min of driving the car the next day.
