I would recommend multiple small rats instead of one medium rat. I have found that colubrids need smaller prey items than an equivalently long constricting species. I feed my 7-foot long Spilotes rat snake 3-4 small rats every 2 weeks.
I would get the bull snake eating frozen/thawed as soon as possible. This is usually not hard with bulls as they are eating machines. Give him 2-3 small rats once a week. As he builds up muscle and size you can consider moving to mediums or feeding more small rats. If you give him a huge meal at his thin size, he is in danger of regurging it and being put off of food even more.
Now, let's address the cage. That cage looks to me to be too small for a snake his size, at least judging by how crowded it is. Get rid of the cardboard box hide- it can grow mold and bacteria...not good for snake health. Invest in either an opaque plastic hide or a naturalistic snake den. I personally like these, as they are very natural-looking and snakes love them. They are also non-porous so they are easy to sterilize.
Hiding Cave - X-large - 11 in. x 11 in. x 4.75 in. | ThatPetPlace.com.
Next, you need to have a water bowl large enough for the snake to comfortably coil up in. To save space, I like to use corner bowls for larger snakes. They are easy to clean, blend in well with cage decor and are very durable.
Repti-Rock Corner Bowl - X-Large - 14 in. x 14 in. x 3.5 in. | ThatPetPlace.com. This will allow your snake to soak and hydrate himself. The other thing that such a large bowl will allow you to do is to check for mites....if the snake soaks, dump the water out into a stoppered sink and look for what will look like black sesame seeds with tiny hair-like legs. These are mites.
My suspicion is that the scale damage is caused by irritation from a long-term mite infestation. Snake mites are tiny and can be very difficult to find on a speckled/blotched patterned snake like a bull snake.
What bedding are you using? It looks like cypress mulch. Make absolutely sure that any bedding you use does not contain pine or cedar...these aromatic woods are very irritating to snake's skin and respiratory tract and can be fatal.
Best of luck...keep us posted.