Mysterious Bald Spots...bully cat??

PLEASE BEAR WITH THIS LONG WINDED EXPLANATION: I'm hoping someone might have some insight into a problem I'm having with my 3 yo female cat. About two months ago she developed two semi bald spots on her side (and later a third on her other side) which I suspected she did herself, either due to stress or compulsive over grooming. I took her to the vet where she was tested for fungal infection (negative), checked for fleas (negative), given a cortisone shot (which did nothing really). I also switched foods to California Natural herring and sweet potato (in an attempt to rule out food allergies). I also purchased a feliway as I've used it in the past and it seemed to help the overall behavior of my then 3 cats. Well I am down to two of those three, the two who have never really liked each other (due to a breakup, not a death or anything!). Well the missing kitty was kind of the friend to both of mine. I mention this because I kind of suspect that my huge male cat is behind the missing fur on my little girl. I only suspect this because the newest bald spot is on her back/neck between her shoulder blades, somewhere she can't really lick and get to. Has anyone else had something like this happen or am I crazy and missing some other possible issue that's resulting in the bald spots? Any insight and/or advice as to what to look into/research/suspect would be GREATLY appreciated.