Alan
It seems there is a new regime for Wegener's Granulosis and I hope this will help you. It is very important that you take the medication and it will take time to feel better. Check about this new regime with your doctor. Specifcially I read that Cytoxan that is taken orally with prednisone until you are in remission can then be switched to methotrexate for two years and tapered off. This has been reported to be effective and less toxic than the traditional long-term Cytoxan treatment. And that may help you feel better!
I do suggest you talk to your doctors.