I will try today again, and smooth the stone for a few mins with the 2k. To be honest the stone wasn't totally smooth while honing, I had a feeling like there are a few small particles here and there. This feeling was very strong after 400 lapping, but was almost gone after smoothing, but not totally. The 5k compared to this is like a piece of glass, silky smooth all the way, without any smoothing with higher grit stones.

I am 100% sure that the scratches come from the 12k, I have did even mircobevels to confirm this. The mircobevel which was formed had the same deeper scratches, and a few microchips too.

I will try to lap the 12k to the point where I don't feel any weirdness while honing, I am pretty sure that this will solve my problem. I am just a bit surprised, because a lot of people are using their shaptons lapped with 325 DMTs and 400 Atomas, and they didn't have a problem like me.