You run a lot....Which means you burn a lot of calories, so if you want to put on size you need to EAT a lot.
I'm not even going to guess how many calories you would need to put on size, but if your running that much you might need 6000 - 8000 cals..This is just a guess, someone else might know better..
Once you do start to increase your calories, don't worry about getting fat, it just wont happen.