Dani -
I didn't have skin grafts. The doc did thin the skin and scrape it. He also took out something (tissue, maybe?) from around the hole where he placed the abutment. At first the area was a little sunken in from the rest of my head, but with time, as it healed, the sunken area no longer exists - it's become flat. My site sounds a lot like yours.
I, too, have screws from my AN surgery very close to the surface of the skin on my BAHA site, but the doc said if the heads of the screws pop up completely, he'll just unscrew and remove them. The closeness isn't causing me pain though.
Maybe like you say, there are nerves involved in this problem. I know that originally I had a lot of itching post op and my doc said it was because of the nerves involved.
You might want to check with another doc who does BAHA surgeries and see what his take on the pain is. I can't imagine this is something you will just get used to and if it's preventing you from wearing your processor, IMO it should be fixed in some way.
Jan