For question 3 — the things that reliably make it worse, all of which are what a guilty human wants to do:
Following her. Going to find her, crouching down, reaching out. From her side this is the frightening thing pursuing her, which confirms exactly the prediction you are trying to disprove.
Picking her up. Removes her ability to leave, which is the one thing she is currently relying on.
Treats offered from the hand, too early. The food is good and the hand is the problem; forcing them together while she is still wary can attach the wariness to the food. Put the treat down and walk away instead.
Apologising out loud, at length, in a concerned voice. Tone carries. An anxious, insistent voice directed at a cat is not reassuring, it is more input from the thing she is avoiding.
Two days is short. Most of these repair within a week if nothing pushes.