there are prescription dog foods that are all natural
and taste really good that you can get. I'm sure which
one you would put him on you could ask in a good
pet store or ask your vet. if you are feeding him can
wet food then that might be some of the reason he is
having problems. my dog had almost the same problem
and i boiled him chicken and chop meat drained the fat
and mixed it with some water to make broth not fatty
and cooked him white rice or some pasta and mixed
it in. you can also mix that with the natural dry food
so you are sure he is getting the right nutrition. my
dog couldn't eat dog food at all so i cooked for him
and we didn't have any problems. there are web sites
you could go on to get recipe's for him.
References :

For dogs with sensitive stomachs I use daily slippery elm powder and aphrdophlis yogurt also pro plan sensitive skin and stomach. A cavalier girl that I know can not change her diet as she gets very loose bowl movments untill it turns to blood. All she eats is pro plan (as above) the yogurt and plain sausage (boiled) a very bland diet but it stays inside long enough to be worth while.
References :

I would try California Natural. It has the lowest ingredients ever to help with hypo-allergenic pets. Maybe its something in your dogs food that still isnt helping her. Try this; no fillers, by products, corn, wheat or soy:
http://naturapet.com/brands/california-natural.asp

Also Innova EVO has a high protein level so will help her pack on the pounds:
http://naturapet.com/brands/evo.asp

Its expensive (I pay about 50$ for a 40lb bag of Innova — but I have to small dogs (under 12 pounds)) .. but as long as your dog has some type of relief it will be worth it in the end.

Put in your zipcode to find where to buy: http://www.naturapet.com/where-to-buy/

You can also take the list of ingredients to your vet and see if he thinks either of these foods will help.

Hope that helps and Good luck!
References :