I would suggest taking him to the vet right away. Ball Pythons in general dont like their heads being touched so they flinch back and it could be a natural reflex. When ball pythons start losing body mass they tend to lose it toward the front of their body first and is often an indication of an infection of some sort. I agree with Smynx IBD would have done him in very quikly in a matter of weeks. You have had Runt for a long time and I dont think he could have gotten IBD if he is housed alone and none of your other snakes show signs of it. I think that he may have an internal parasite. Again I say take him to the vet and in the mean time make sure he is not dehydrated and up the temps just a little bit.

Its hard to say exactly what it is. But taking him to a vet would narrow it down.