(most sites can't tolerate my long comments can they? Least I found a loop-hole this time. x3)
Don't know if anyone has reported this yet; but there seems to be a problem with Aela & Lord Harkon on the quests "Proving Honor" & "Blood Oath" was it? The respective quests involve you becoming a werewolf or vampire lord; although I'm sure your aware. The problem is that after you "wake up" the respective Npcs revert back to their respective race & don't turn back to ponies after you've completed them. Harkon I can deal with, he's not going to live for much longer *evil laughter*. But Aela, being a follower & all would be an issue later on. I would use console commands, but did that on one save & it sort of worked, except she was a pony with a giraffe's neck. (plus, I'm more for a permanent solution) If I were you, I'd look into the quest data for those two quests; it might have something to do with they had been different races before you blacked out. (werewolf/vampire lord) I may not be familiar with skripting or mod codding, but I think the code may be changing those Npcs back to their default race rather than their custom race.

Other than the fact that very rarely, random events (imperials with stormcloak prisoner, ect.) sometimes are not ponies; the mod works great. I even got it to work nice with EFF; no idea how I did it though.

(btw, how'd you edit the races in the way you did? Might need to know just in case I use any mods that add Npcs. (I'm a beginner modder btw)