i just had a similar problem i took my snake to the vet, i was given these intructions...
1. use indoor outdoor carpet for substrate
2. take all water out of tank
3. soak ten minutes in clean water then ten in betodine (tea color) water then rise off
4. then apply silver burn cream after completely drying off
5. then every 3 days a shot of antibiotics
My snakes scale rot was the same or worse then yours. the vet visit may be expensive but its compeletly worth it! the visit itself was 75, the cream was ten and the antibotics were 10 for a bag of about 25. My fella has gone throw one shed and is already looking ten times better. make sure to keep him dry in his enclosure!
alright sounds like a plan but may i ask what kind of antibiotics were given and i'm headed to get the cream later today