I know you stated that your husbandry is perfect, but to help get a better overall picture, would you mind sharing what the set-up is - the type of cage, the temp - hot spot, ambient, type of substrate, humidity level, what was it that caused you to determine it was scale rot and how was that treated? Was the "scale rot" on the belly only or ?

I would definitely look into a visit with a vet.  If he's been in your care over 2 months, and is still having issues, it really couldn't hurt.

Likie Sonja said  tripple check your husbandry  and watch the "bruise " if it gets worse  a vet trip may be in order

I have him in a 55 gl glass with a screen top partialy covered with foil to keep in humidity which works amazingly. (stays around 50% before misting twice a day and 70% after) I have an ambient of 80, basking of 95, undertank belly heat at 85, and his gradient goes to 70. He is bedded on coconut bark chips and hasn't eaten on it for sure. He was determined to have scale rot due to the small pink splotches on his belly along with soft wrinkly scales on his belly. (a mild case) which i was told by a vet proper husbandry would cure up itself with a couple of sheds. He did have a strange small poop at one point that consisted of a skin like substance with what looked like small granules of a substrate. I couldn't get the man to remember what kind of substrate he was using. He just said it was something for snakes from the pet store. :p He has a huge half log to hide under to feel secure so I know after to months he isn't as stressed as he was. My boyfriend had him out yesterday and we noticed he had more interest of his surroundings and even grasped onto our arms, seemigly alot stronger than when we purchased him. He still pretty lazy about his habitat though as at night or really any time of the day he doesn't move much. :) Thanks for the advice that was given so far guys. I will have him to the vet by I hope friday if they can fit me in.....

Well after searching around for forever i found an exotics vet about 50-60 miles out so he goes this wednsday (as soon as they could fit him in) to see what's going on with him. Also taking my little ball python just to be sure it is healthy as well. Thanks so much for all the help and Joe we had stopped handling him as I agree it could cause extra stress. I will be posting results as soon as I know. Thanks a bunch!