Mass would be a result of changing their tissue weights, the body size modifier is volume and all regular ponies are roughly the same size, so I can't do what I did with cave ponies. It might be an idea to give pegasi lighter bones, yes, I'll have to see about how to make that work, since it'll be swapping out bone materials based on caste.
It might well be an idea to increase the skill rate debuff on pegasi. At the moment, they're 20% faster, and learn 10% slower. It's odd that they learn faster than an earth pony who learns 30% faster, though.
Parasprites are quite small, about the thirtieth of a dog's size. It's possible the dog got swarmed by a number of parasprites, making it easier for the sprite to get a decisive strike in, or it could just be random chaos, "If there's a storm in Manehattan, a parasprite tears a dog's throat out in Ponyville". In any case, unless events like that one are more common than I realise, they should be working right.
Edit: I've uploaded the fix for doughs and the gynosphinx stuff, you should just be able to drop reaction_pony_dough.txt and creature_pony_lion.txt into your main and save raws. I'll update the OP, it's still go the version 1.4 data.