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Help with my sounds

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If anyone can help me with this issue, I'd be very happy! I recently (3 months ago) rescued a 2.5 yr. old Sheltie. THis poor girl was with a breeder who got her from someone that didn't give a flip about her. She was left in a kennel 24/7. Only given food and water, no human contact. When the breeder got her, she was left alone, bred for puppies, and after the puppies were sold, she was put outside and basically got nothing. Now, she lives inside with me, and knows nothing and scared of everything. We went to our first training class for clicker training and the sound scared the living daylights out of her. Ok, I brought her home, tried everything with the clicker, even wrapping it in a sock, she was terrified. So, we tried an ink pen. That scared her too, so I tried just making the noise with my mouth. Same reaction. What can I do now? Every little noise scares her. Should I hold off for awhile longer? Keep making the clicker noises? What? I'm at a loss, and would love to teach her to at least not bark all the time. She is smart, no doubt, that is the Sheltie in her, but I want her to relax! Any suggestions would be greatly appreciated at this point. She has come far in 3 months. Learned a new name, sits, is now housebroken and has bonded to me. She seems to lack confidence and there maybe a trust issue too, I'm just not sure.