Good on you for sticking with that runt. I have binned a few seedlings that showed unusual growth characteristics. Instead of two sets of fans, I had something resembling an ear growing on a couple of Skunk sprouts. Like one big leaf. I am gutted I chucked them now. I had it again with a cheeseX and stuck with the seedling. It took a while to sort itself out but when it did, it grew into a beauty. When I flowered it, it exploded with bud and trichs. The 'normal' looking phenos had nothing on it.
Good luck with the grow and getting seeds with that male.