Seems like quite a nasty skin disease going on and now that he hasn't responded to conventional treatment, you will have to prepare for some more advanced diagnostics or prepare yourself to be referred to a skin specialists. Steps to be taken now by either your veterinarian or a dermatologist will need to involve another skin scrape and consider a fungal and bacterial culture of the skin, running a blood profile and a viral panel to check for any underlying disease or immun deficiencies, a skin biopsy. This is likely the only way that you may get to the bottom of all this and know whether or how long the problem is going to need to be treated. A behavioural stress related skin disease may also need to be considered. Speak to your vet about these options, or ask him about referring your cat.
Martin Slome DVM
Centre Street Animal Hospital
7700 Bathurst Street Units, 40-42