My poor shelties skin condition

Question
My Sheltie, Cooper has been suffering from a mysterious skin condition for over a year.  The symptoms are: oily itchy skin, fur discoloration (Cooper is a Tri, and his fur is turning brown) red scales, and loss of fur around his neck or ruff. We've had many tests done which included skin biopsys, but to no avail.  At one point the vet and I concurred that it was a systemic yeast infection, and we started treating Cooper holistically (pro-biotics) as well as with western meds ( a three month course of a human fungal medication).  I bathe Cooper every week with Maalsab (making sure to keep the shampoo on him for at least 15min).  The bottem of his paws are red, and he licks them a lot. He doesn't like to go for walks on any hard surface, but we do still have fun chasing tennis balls on the lawn every day!  Near the end of last Spring he started to show some improvement, less scratching and less "nasty" skin odor; however as soon as June rolled around he became miserable again.  The vet has again prescribed the fungal medicine, and I've been giving him an antihistamine twice a day.  Autumn is almost here so we're keeping our fingers crossed.  Oh by the way, my old vet thought that it was a food allergy and as a result of that diagnosis Cooper has been eating high end canned food, free of any fillers; I also give him yogurt and boiled chicken.  Any ideas?
Thanks so much for your time.
Sincerely,
Monique Nemarich

Answer
Monique,

I am so sorry to hear this.  My suggestion is to have your vet contact the nearest veterinary school and ask them for help.  There are nasty bacterial infections that can cause this.  Perhaps you have a tougher than normal bacteria that is resistant to the drugs that are available?  I would not hesitate to take this dog to someplace like University of TN school of veterinary medicine to see if those minds have any insight.

In place of high end canned food I might suggest a diet of rice, peas, carrots and chicken (no bones) and the yogurt with a dog specific multi vitamin.  That might actually be cheaper and better for him than the canned food.

Miscellaneous thoughts:
If you quit the otc antihistimine for a few weeks is there any worsening of his condition?  
Any allergy specific tests have been run?
What kind of detergents are you using on your bed/clothes and his bedding?

Please do update me.  We will keep you in our prayers.

Dave