Oh, how heartbreaking. All you want to do is love her and make her feel comfortable, but she is too afraid to allow it.
I went through something similiar with my puppy mill rescue, Lane. She would hide out, but she also would have the tail tucked/pacing/panicky thing happen with no apparent trigger. It almost seemed like a form of PTSD. I know one trigger was after pest control had sprayed our unit while we had been gone all day. I do think a journal is an excellent idea.
What actually helped Lane a lot (along with time and my other pup Rory showing her the ropes) was when she'd have an "episode" as I called it, I'd put her in one of her carriers. She felt safe and secure in her carrier, but she could be moved from room to room with us as we did things and was still part of the group. It seemed to help Lane, but, of course, every dog is different. I remember I'd let her chill out in her carrier next to the food bowls as I'd prepare their meals, and she would watch me intently. Then I'd place her carrier on the ground and open it up, so she could go eat when she was ready. For the most part, she had very few episodes where she was this scared, because she'd be fine for months and months at a time, and I never did figure out what triggered them.
Good luck to you and sweet Lilly!