Need serious help...clear details to follow

This is probably an easy one for some of you. I thought it would be easy for me, as this is not my first rodeo with new kittens. I am honestly lost, though, and could use some help because I'm not ready to give up just yet.

Two weeks ago, I adopted two eight-week old female litter mates. I knew it was too early, but the guy seemed determined to get rid of them any way he could, and I figured, better me than the street. Technically, it could be called a rescue, since the previous owner kept them outdoors, allowed them to roam a neighbourhood filled with stray cats and high-traffic thoroughfares, and fed them dry, adult cat food as soon as they were weaned. They were both underweight, dehydrated, brutally infested with fleas, riddled with both round and hook worms, and had colonised so many ear mites that one had scratched clear through the outside of her ear. I took them both (mostly to get them out of there), and two weeks and a $300 vet bill later, they're healthy.

Here's the problem...while one, (the calico in my avatar) has adapted well, and loves treats and cuddles. The black and white one positively disdains human contact. She runs, hides, and hisses when I come near her. She hasn't learned to use her teeth and claws to fend off a human yet, but it's coming. She is litter trained and did well for a few days, but then took it upon herself to use the couch instead, with her sister following her lead. They would get up there and pee TOGETHER. I was already diligent about the litterbox, but I started being diligent twice a day while they ate, so it would be clean when they finished their meal. That's when she started peeing on my bed.

I understand that this kitten is not human, and therefore has no understanding of gratitude. I understand that she has to learn not only cat-behaviour, but cat-owned-by-human behaviour. I also understand that she has never had a good experience with me. I show up, take her away from her mother and home, pack her into her first carrier for her first car-ride, bring her to a strange place, give her a flea bath, flea-comb her, brush out her fur, (they are both long-haired cats), take her to the vet where she is poked, prodded, and given shots. Then I bring her home, give her nasty-tasting medicine, and twice a day, every day (still) hunt her down, snatch her up, and put drops in her ears. She really has no reason to like me.

She is spending all of her time in the bathroom. I cannot leave her out when I cannot watch her like a hawk. I can’t let her out when I’m uncertain of being able to catch her again, and I can’t catch her alone. My roommate and I can’t catch her together, and it’s at that point I feel like I’m terrorising her. I feel like a terrible pet owner, but I don’t know what else to do. I take her out for five minutes at a time, and put her in my lap. I pet her and talk softly to her. I offer her treats, and even made her purr once, but just once and I’m pretty sure it was against her will.

I don’t force her. If she is freaking out, I let her down…in the bathroom. She has all of her toys in there, as well as food, water (on the opposite side of the room from her litterbox), her “baby blanket”, and more treats than are probably healthy because I feel guilty. She still runs from me, hisses when I come to close, and even when she’s just sitting in my lap, it’s like this frozen paranoia with her ears laid flat like she’s just hoping I don’t eat her before the perfect chance to escape presents itself. She needs the medicine, and I try to be soothing when I do it, but she’s not having any of it. I feel like I’m permanently damaging my relationship with this animal.

However, in my mind, these traits make her unadoptable. No one wants a kitten that avoids them like the plague. Anyone I give her to may be disappointed or frustrated enough to just put her out. She is 2.2 lbs, female and un-spayed. She would never survive, and I won’t take that chance. I need serious, valid advice on how to socialise this animal so that she and I both can be less stressed out in our own home.

**I’m sorry for being so long-winded, but I figured a clearer story would help some of you cat experts put a solution into more solid perspective. I’m also sorry if this, maybe, should have been posted in the Feral/Rescue forum. I think I was hoping that this forum would net more people who might be able to help. As always, thank you for any help you can offer. I appreciate you.

First I want to thank you for rescuing these little ones. You are correct to confine her. In fact I would put the sister in with her until both are using the box consistently. To tame her, you could try going into the room when it isn't time to medicate and just talk quietly to her, or even just read aloud to her. Give her time to see you are not an ogre that is going to eat her. It would be good if your roomate could also talk quietly and read to her. Don't try to touch her during these sessions, just let her make the first move. Try to keep the two together as much as you can - you don't want to have to re introduce them later. Make certain you clean everything that they urinated on with an enzyme cleaner to remove all scent. I hope some of this helps.

Yes, first thank you from helping these kittens. @posiepurrs has offered excellent advice.  I would add that, while I totally understand your frustration, it has only been two weeks and it's likely you are going to have to be VERY patient and give her A LOT of time to come around.  I know this probably isn't exactly what you want to hear, but cats can take a long time and have great difficulties adjusting to change, and I suspect that is part of what is happening here.

Once she is more comfortable and out of the bathroom I'd add some more litterboxes if the urination problems persist.  It sounds like you may have only had one before, and with two cats at least three are recommended and that might help.  Some cats don't want to share boxes no matter how clean they are; others need different ones to pee and poop in and won't do both in the same box. I know it can be annoying but it is MUCH easier to accomidate the cat and add more boxes than try futilely to change their innate preferences.

Good luck and please come back with updates or if you have more questions.  We are here to help!

So I followed the advice previously given, and since I'm still giving them the ear drops...it's a temporarily lost cause.

Tonight, however, the skittish one (who still doesn't have a name) escaped the bathroom. I left her sister in there and let her stay in the living room with me as the only company. I didn't approach her, just talked to her from across the room in my most non-threatening, and non-ridiculous, voice. I tossed her a treat, and discovered a behaviour that had been difficult to see when the kittens were together.

She leapt to the treat instantly, but then froze. She spent five whole minutes crouched over it looking everywhere at once. Her ears were laid back and then up, then back, then up. Her eyes were wide and alert, her head cocked to every sound. And nothing changed for five minutes. Then she licked the treat and started scratching the carpet around it as though she were trying to mask its scent, like in the litter box. She disappeared after that.
Another five or so minutes later, she re-emerged, approached the treat cautiously, and then ate it. The same behaviour resulted from a second treat. Only now she's running about, acting fierce for no one. She will run up to the treat, put on a show, scratch around it, and then start tearing around again.

This feels to me like an animal who is paranoid about bigger predators. Testing the waters to check for competition. Maybe a memory?
How far off am I?