I personally would cease meds in the quarantine tank do PWC and run fresh carbon.
The meds may be causing the internal problems you suspect and on top of that the stress may be the reason for not eating. The stress and meds could also be a reason for the paleness.
The flickIng and rubbing has stopped so maybe that's an indication that the external irritation has ceased.
I've had 4 fish over the past month going towards food but not eating but mine lost weight and looked pale. I've had one fish stop eating and bloat wich I'm suspecting is caused by the damage of over medicating.
Bloating is usually associated with organ failure causing lack of osmotic regulation.
There is now no medication in the tank at all and the GBR has been facing the same direction, just above the filter head for 3 days in a row, only to move when I removed the aquarium lid to answer the burning question "what the **** is this fish playing at?"
There is absolutely no rubbing/flicking and there is no appetite. However, the GBR now has a whitish tint to the front dorsal fin and is swimming with it's head down. Fish constantly has a 'black tar mark' accross the central part of the body which is associated with stress/being scared.
With regards to the gravel vac advice, I always do gravel vacs on a weekly basis. I cannot add activated carbon as there is no such part to the filter system for this.