After about 6 or so hours of tweaking I think I finally managed to find out what was causing my issues in VR, and have a stable 45 FPS throughout the whole game.
I have a high-end PC, and I was getting 22 FPS on the Supercarrier decks (in certain scenarios), along with other areas with high traffic (mainly on the ground). I was also getting a really bad stutter when looking out the sides, along with flutter/ghosting. It was happening the worst when I would start at a cold start on the carrier deck. Looking forward, right, up, back I had a 45 FPS on the ground. When I would look to the left, even slightly, the FPS dropped considerably. In flight, when I looked at the carrier, the FPS would drop to a nauseatingly bad level.
End result: turning OFF shadows completely solved the FPS issues. I am able to run some really descent settings after I did this. I also forced the ASW on through Oculus Debug, which helped with the stutter/flutter looking around.
Perhaps ED can look into this and fix it to have the shadows back?