We've had a horrible time with rain rot for the past two years. Over that time we've amassed an arsenal of anti-rainrot treatments. Here's what we've ended up doing:
-Wash it with iodine shampoo every day (go to twice a day if necessary). -Scrub it in really well to loosen the scabs (I prefer this to picking it off, and it seems more comfortable to him). Wash it off, then dry it really well. Use a hairdryer (low setting) if you have to, just get it as dry as possible.
-Then apply MTG liberally.
-Do this until the area seems to be flaky, rather than scabby. Then switch to Infusium, a hair conditioner you can buy in your local drug store.
After that the rain rot generally disappears, with us. Frosty might be a special case, and it's certainly not easy to treat him since it takes forever, but this might work well for your horse. :)