tl;dr: https://www.reddit.com/r/VFIO/comments/78i3jx/possible_fix_for_the_npt_issue_discussed_on_iommu/
I startet messing with GPU passthrough again and made a couple of changes:
The host 560Ti is now in the bottom x4 slot. Getting Fedora to claim it as its primary video is actually pretty straightforward considering the archwiki states its impossible.
This leaves the second x8 slot for a SATA or USB Controller. Currently its the latter one, I had issues passing through ASMedia based SATA cards, a Marvell based one is on its way here for further testing. Hugepages gave me more stability but not quite the fps improvements I was hoping for. While doing research about further CPU tuning I stumbled across the proposed patch linked above. I will give this a shot, just wanted to let you know about this, if you want to tinker with this aswell. More on the story as it develops…