Cat Is Scratching Herself Raw?

My fur baby WitchCat is about 9 years old and we have had her since she was a baby. She is an indoor/outdoor cat. We give her the proper meds to make sure she doesn't get fleas or any kind of parasites. We also have her on a controlled diet with food that helps with weight, since she is a fatty, and coat health. We noticed she started getting what we call "boo boos" around her neck after the first few years after her first litter so probably around 2 1/2 to 3 years of age. At first we thought she was still promiscuous and the wounds where from other male cats. It wasn't until recently that we found out she was doing it to herself. We had her stay inside for about 2 weeks because of the weather and we noticed wounds not scratches or cuts, but pieces of open skin bleeding all around her neck and now she is moving on the top of her eye so around her brow and even her cheek. We where thinking maybe it was because she was stressed, but she didn't act any differently and we never caught her in the act. Like I said she is a very healthy cat and has no problem being left alone, she prefers it usually.

I was wondering if there was a reason for this. I've read about parasites and fleas and honestly don't think that is the issue. I also read about food allergies, but she only eats the food she's been eating since we first brought her home. I really would like to help my little girl. The wounds are very itchy because when I clean them she starts trying to scratch that spot.