I run into this ALOT. I work at an animal hospital grooming alot of farm dogs and some smaller animals people do not have the common sense of how to care for them. Unfortunely some of these dogs have a horrible odor. Its almost impossible to get out. Its most likely in his skin pores. Its mildew. I will try to give you the best advice I can possible give.
1. This is something most likely will have to wear off.
2. Start over. Shave him down close...all of it. ( i hate to be the one to tell this and it is a horrible cut)
3. First wash him in dawn dish washing liquid. I know seems harsh. Let him soak. Rinse as usual.
4. If that does not help. Use vinegar. Apple cider is the best. The acids will help break alot of the stink down. You may have to do this each day.Don't rinse off.
5. Let him air dry and rub some baking soda on him.
Hopefully this will help. I've done alot of reading and alot of practice with this. Although, getting the client to do what I ask is a different story. They are farm dogs.
Good luck!
Let me know how it works for you.