Sounds like you're doing pretty well! Have you had Loki checked over by a vet to see if there is any physical reason for him not liking being touched in certain areas? Does he only dislike being touched in these areas when he is eating? I personally wouldn't like a dog in my home to growl at me for any reason, but then I do have kids. If you are happy with the situation then that's great, but I'd still try to get him not to do it if it's at all possible just incase he ever has to stay with someone other than you...vet, kennels, relative etc.
I would get him checked over by your vet and if there is no reason for him not liking having certain areas touched then I would keep trying to touch them to get him used to it. Try it when food's not around him, groom him all over, pick up his paws, rub his ears, praise and treat him for allowing you to do this without growling. He's young enough that you can get him used to all these things and it makes him far easier for a vet to examine him should the need arise
