Sounds like she is doing really well and making great progress
But PLEASE do not use the pebbles in a tin suggestion, or any other aversive method. As a site COL promotes only positive, reward based training methods.
Given that she is still so nervous and is making slow progress, anything that gives her cause to be fearful of you or her new surroundings is bound to do more harm than good and could undo all your hard work so far. It is important to reward her for good behaviour, rather than punishing her when she does something you do not like. No doubt at the puppy farm, they were left to bark, so it may be a hard habit to stop.
Cockers are a vocal breed, but if it is a problem, you can train her to "speak" to order and then "quiet" - rewarding at each point. Have you tried distracting her from the things that she tends to bark at with a tasty treat or game? Distract her when she is in the situations that cause her to bark and reward her for being calm. If she is reluctant to take treats from your hand at the moment, you can try throwing them on the ground near her.
To be honest, given her background, anything that suggests she is becoming more confident in her new environment sounds like a good thing, but like everything else, time and patience are the answer.
You may not be able to solve all her "issues", but it sounds like you are doing brilliantly so far