This is OP here, since I hit the maximum reply’s per day for a new account I wasn’t able to post this before. (Hence this temporary ALT-account)
Problem solved.
I want to thank everyone for their time and help, especially @Urquhart who tried solving it with team viewer with me.
This new build has been a huge problem since I put it together a week ago. I’ve literally taken this PC apart into individual components and put it back together around 8-9 times now.
There was always a strange lag in windows and KDC took a very long time to load and random unexpected very high cpu usage, even though other games ran with no problems and high FPS on Very high quality (like Shadow of the Tomb Raid was 80+ fps on all max settings).
After everything I have done before I went through my logs and saw Java 40% CPU usage a few times, but not the only program doing this. This high CPU usage was almost random on what program set it off.
What ended solving this was downloading Win 10 install to USB and installing it completely from scratch, onto a different SSD (so I wouldn’t loose my personal files on the original).
Now everything works like it should. I get 90+fps on ULTRA in KDC and all input lag in windows is gone.
Again, thank you all for your help and time.