Along with having epilepsy, I'm also a qualified Sports Therapist and Deep Tissue Masseuse, so have dealt with some similar sounding issues.
The length of time you've had the injury, will likely determine the issue. Firstly go and see your Dr to get you referred to a specialist, likely an Osteopath or Physiotherapist. If there is an issue with your back but it's causing you pain when you're coughing, my best guess is that you've torn a muscle in your mid-back section, or had a fracture/break there, otherwise you'd be feeling pain in your neck as well. Getting properly examined by a specialist will be able to determine exactly what the issue is. Bruising is unlikely, unless you had the fit a matter of hours/days ago. What I will say is if it's been caused by a seizure, it's not at all likely that it's an issue to do with any immune issues, arthritis etc, but rather a temporary chronic injury, that with treatment will heal nicely. Extreme trauma will not cause an injury that won't heal with time and treatment. I had a friend who had a badly fractured rib and wasn't aware of that being the cause of back pain until 2 weeks later, but she's back now after 4 months to full health and playing rugby again.
Re your remedies, it will completely depend on the injury. If it's muscular, a Deep tissue Therapist or Sports Therapist will use massage to not only help heal the injury, but make sure that after the muscle heals in the normal mesh it makes naturally, that they encourage the muscle back into long stripes, making if far less likely for the area to re-tear. If it's bone, kinesiotape and massage to stop the muscle tightening round the area to remove the pain that will come with it, along with rest will be the best help.
I wouldn't recommend work in the water, unless supervised by a physiotherapist, incase you inflame the injury further should your arms be pulled backwards with the water through the natural swimming strokes used from my experience.