Unfortunately I've messed up and don't really know how to remedy the situation, I need some suggestions and help.
The situation is as follows: my in-laws are vets and do a lot of pro-bono work. One day they had a small (feral) kitten in their clinic that had suffered a rectal prolapse and had been brought into them after being found and (unfortunately) after she'd seen some rough treatment at the hands of the cattery's resident vet, that had apparently stitched her anus shut without anathesia. Anyway, once they remedied the situation and repaired the damage, she was a fairly normal kitten and I took a shining to her, so after a few months that she went unclaimed I took her home.
She's developed normally and is now about a year old. I've had her for about seven months now. She's extremely skittish and has always rushed under sofas and beds to keep out of our way, but simultaneously seems OK with us when we're stationary and she is being the active party. Honestly she seems better with my partner than with me, but then again she has a good way with animals. The cat has her litter box and uses it very effectively, eats and drinks, plays around with stuff, and often sleeps with us. First thing in the morning she's always very affectionate with head bumping, licking, and miaowing.
Anyway, I was trying to use the "gently confine a kitten" method to teach her she had no reason to run under the furniture all the time. That wasn't working so while I was at it I decided to comb her because she was shedding loads. She never much liked that and probably that was the wrong thing to do because it lead to her suddenly defecating on me, which lead me to scream and jump up, she ran scared, etc., and then I tried to catch her because she was leaving shitty skid marks wherever she went.
That must have terrified her and I regret it. Now she's extremely wary of me (I don't blame her, I would be too) and whenever I approach her in a manner she deems threatening (quite difficult not to approach her in a two-room apartment) she pastes herself to the ground, puts her ears back, and flicks her tail in a classic display of submission. She becomes totally non-interactive so I can't even successfully get her to take a treat and defuse the situation. She's never been the smartest cookie in the jar (sometimes can't even find treats that are offered to her on the palm of one's hand).
Anyway, I know I screwed up, and I would like to know where I can begin to rectify the situation and regain her trust.
Thanks for taking the time.