Hi,
My present GR also has pretty major allergy problems and as my husband is in the forces we move around quite a bit. This means that veterinary treatment has been of limited use, well none actually! Our local vet at the moment is very keen to start sticking needles of cortisone in, a substance that drastically reduces the natural immune system. As I know to my dogs cost this is an invitation to every harmful bug around to have a party on his skin! This vet has given up and said this is the only thing he can think of.
A few things that have helped Paddy; diet, add a raw egg once or twice a week to his feed (if he is not allergic to them), raw minced garlic, 1 or 2 cloves a day, brewers yeast, invaluable and a cold pressed vegetable oil, start with a tablespoon a day.
It is vital that the cysts are dry at all times, clip any excess hair from toes and under and between pads with blunt ended scisorrs. Try splitting your dogs daily intake of food into 3 or even better 4 small meals a day. Before each meal bathe the cysts in a solution of Epsom salts and dry thoroughly then try a nappy rash cream such as Sudocream - a tiny bit goes a long way!! Rub this well in and then take a very long time preparing the meal, time the dog is not thinking about itchy feet!
Distractions are also a good idea although beware of anything that will stick or dribble onto his paws, Kongs stuffed with food and then frozen are brilliant for times that there isn't anything else to do, but be sure to remove these as soon as something more interesting happens. These are good if some garlic is added to help a blind dog find them!!
Hope that is of some use, good luck!