With your settings, and with my above limitation to start the game in 1280x1024 (which is not important because only the d3d9.ini resolution is), after restarting computer fresh, it takes me 4 minutes 20 seconds to load the "XXI Erprobung" mission.
Ahnenerbe's fix has some glitches when mousing over some u-boat locations, they don't always work, but that's it, no other trouble to mention.
Don't mistake me: it's fully worth waiting that long, because you get to see a really awesome game after
I hope you can somehow diminsh that loading time.
My Nvidia Control Panel settings for scaling are:
Fullscreen with Display (not by GPU).