i think there's no harm in trying to get some cardio and arm strengthening exercises into your life at all.. as long as like you say, you protect your abdo muscles. does the gym have a qualified (medical) advisor? i think that's the way i'd go, ask advice from an expert and explain what surgery you've had & how long ago.. and get a tailormade personal regime.
the hernia pain.. i can't remember feeling it for the first time, but basically it felt like someone or something was pinching hard below my skin in one spot (about an inch from my stoma towards my belly button). i think it probably started out a small tear and grew, because in later months if i coughed or sneezed, it bulged out a lot and at those points the pain was excruciating - i automatically learned to push the lump back in with my fist. that's when surgery was deemed necessary.
i would say if you're getting a general all over ache, then it's probably not a hernia.. it could just be nerves healing, after effects of surgery, but still worth mentioning to your doctor when you see him. if you keep on getting a particular pain in one spot, then it could be.
i hope it isn't, but keep a record of the pain, where it is, and what brings it on & let your doctor know at your next appointment.