Do what I did. I swapped in another weather mod, i.e. "widesky" and it not only looked a lot better than the regular vanilla WoV clouds, but it brought my FPS up enough that I am able to fly with shadows and interior mirrors (plus everything else maxed out).
With both the "high" and "medium" YAP2 clouds, I was getting about 13-15 FPS low over the ground, but with the "widesky" clouds, I was getting 28-30 FPS over the same terrain in the same weather conditions.
Are the YAP2 clouds, better, yes, but not 15 FPS better to me when I am trying to max everything else out in the game.