@Eggcessive thoughts?
Does she have an roughen spots anywhere else on her body - legs, thighs, wings?
Was she vaccinated for Marek's?
How old is she?
A vet can hopefully perform some testing or do some skin scraping to determine if this is disease or possibly bacterial/fungal related.
Since she has a history of Wry Neck, is not growing/thriving and has a skin condition, she may have something like Marek's. But its hard to know without testing.
Rule out external parasites like lice/mites by checking through her feathers during the day, then at night with a flashlight when she is roosting, but I don't see anything that looks suspicious like parasites in the photos.
Watch to see that she is drinking well, offer her some poultry vitamins that contain B vitamins and see that she is eating chick starter or an all flock/flock raiser type feed. Egg, tuna, mackerel and meat will give her an extra boost in protein.
Since the cockerel is bullying her (could be she weak/sick or he's acting like a cockerel) you may want to consider caging her in the run so she can have some peace and be relatively safe from unwanted attention, but still remain "part" of the flock..