Molly sounds a bit like my Misty. She's 10, she was a ferrel kitten, only about 7 weeks old when we adopted her, all she did was hiss & spit at me. She warmed up over the years, but she's still very skitish. As long as she doesn't run from Lakota (6months old) they can get close, rub noses and such. But the second she runs, Lakota chases her, and she'll go behind the couch. I try to correct the pup and distract her. Well as if having to deal with the puppy wasn't bad enough, we had the a/c on for about 2 weeks straight. She won't come in the house when the a/c is on. Finally she started coming in to eat, but would sit infront of the door meowing to get out as soon as she ate. I felt really bad for her. We turned off the a/c a few days ago and now she's much happier and she's sleeping in the house. There was a time she did a disappearing act for a few days, but she came back. My older cat is about 17 now, he's trained enough puppies in his life and he doesn't run so I don't have a problem with him.
Lakota - WGSD 1/13/10
Wolfen - WGSD 12/31/14
Bull -WGSD 2-10-10
Apache - Shiloh Shepherd 12/15/02 - 6/9/15
Kiya - Shiloh Shepherd 5/15/04 -12/19/25