Hello, I'm sorry to hear about your kitty.
The hard raised bumps on her ears and face could be several things, from vasculitis (an autoimmune type condition or body attacking itself) to reactions to mosquito or flea bites, or a condition called solar dermatitis in light skinned cats (UV rays causing sunburn and subsequent skin damage).
Another possibility is tumors called mast cell tumors.
While all of these are possibilities given that she has lesions on her haired skin as well I do believe that allergic dermatitis is the most likely cause.Program does work as a flea birth control but it does not stop fleas or other insects from biting her and if she's allergic then these bites will lead to symptoms. In allergic animals I prefer Frontline or Advantage applied monthly.The way to avoid mosquito bites is by keeping her in at dawn and dusk when these insects are most likely out.
To treat her itchiness give her 4mg or chlorpheniramine orally once or twice daily and an omega 3 fatty acid supplement. I like 3V caps or Derm caps. Together these work synergistically to stop the itch.
You can also try applying a small amount of cortisone cream (like cortaid) to the affected areas. If this is related to solar dermatitis then keeping her in during prime sun hours, 10 am to 4 pm, ans using sunscreen on her ears and nose is recommended.If this therapy does not improve her condition in a couple weeks I recommend biopsying these lesions for a definitive diagnosis
This is a picture of a cat severely affected with solar dermatitis
And this is a cat affected by mosquito bite dermatitis
This is a picture of vasculitis (it's a dog but will look similar in a cat)