Got it to this state last night. Took me almost 2 hours, but I took it as learning...
I had to go between 1000 and 6000 quite many times. Every time I returned to 1000 - instant dull grey all over.
Also difficult to see what is beneath that grey layer. So when back with the 6000, more scratches revealed. This happened many times.
At the end I almost felt like crying when most of the grey was cleaned and then saw scrathes again and new I had to go back to 1000 and thus back to a lot of grey
Getting rid of the grey with 6000 was also something really strange. During the 2 hours it seemed when I held the knife 45° to the stone, like when sharpening, the grey just did not reduce.
I tried just about everything - varying the angle (of "knife handle to stone"), pressure, placing of fingers, how much mud on stone and flattened the stone few times during the session.
At the end, only turning the knife to 90° to stone and going with lightish pressure seemed to make a difference and worked the best. Touching up with newspaper also took some of the light grey which the 6000 just did not reduce.
So next time thinning and polishing this knife, I'll get some coarse stone, like Gesshin 400, and also have a go with the nashiji part. Just to get some challange and learn more
Perhaps some extra high grit polishing paste might be worth a try? Or perhaps a loaded strop?