It may be something that needs a multi-prong attack; keep using the Pyoban shampoo weekly, leaving lather on him for 10-15mins and then rinse very well and then rinse again...soap left on the skin can cause some of these type problems!
It generally takes 'moisture' to assist fungal growth (and some bacterial growth too) so I would check what type surfaces this dog lies on most often...is it 'something that can breathe' or is it something more likely to cause 'sweat'? Try keeping a cotton covering under him to absorb body heat/moisture.
I am probably one of the least-informed about food for stones, but others here have dealt with this problem so hopefully they'll chime in here...and there are also websites/discussion groups dealing with dogs that have bladder/kidney stones so perhaps you'll get an internet address to direct you for more info.
How long have you been keeping him on medications, and are they antibacterial or antifungal? A quick check on the internet with the name of the drug should help clarify. Fluconizole (sp?) is a commonly Rx'd medication as anti-fungal but it can be hard on the digestion...if used, give with food and perhaps 1/2 dose in AM and 1/2 dose in PM...check with your vet re this.
Antbiotics are particularly vulnerable to misuse...you must give them to completion because when used for short bursts of time they only weaken a germ, not kill it, and the body becomes resistant to its benefit. Sometimes an antibiotic needs to be changes 2 or 3 times (different drugs) to find one that works well on your particular dog...and they are generally the least-expensive part of treatment.
Are you giving Benadryl antihistamine to this dog? If so, it may make him a bit sleepy but it also relieves itchiness and is worth using...not habit-forming and should not have long-term negatives if needed for the entire warm-weather season.