My Cat Pepper

Ok, I have been told that Pepper is a feral cat. I got her when she was probably less than 3 months old. Her and her 2 sisters had been abandoned. I had another cat at the time (Cinnamon - he is missing becaue he got out of my house 2 weeks ago). Pepper and Cinnamon bonded really well. Cinnamon is a very friendly cat. Pepper would even groom Cinnamon and they would chase each other around the house. Pepper has never seemed to like humans. Pepper is now 2 years old. When Cinnamon came missing Pepper would go around the house crying. This is something she had not done before. Now 2 weeks later and she is getting louder. She will come looking for me and start crying and yelling. Sometimes she will come within a foot of me and then fall over on her side and look kind of silly. But, if I make a move she will run away. The other night she came in the bathroom with me and I shut the door so she could not get out. I picked her up, she only hissed for a second, and began scratching her head and held her for about 5 minutes. Of course as soon as I let her down and opened the door she was gone. Today she has been yelling, crying being very voiceferous but only runs when I try to get her. Any suggestions?