I know. It is so scary when all this is happening and you don't know how to fix it. The fear of screwing up and then something terrible happening is a heady feeling. I am as control freaky as you so I know exactly how you are feeling. I'm sure Kaylee is partially picking up on your anxiety, and that is making her more anxious too.
So, here's some things I would try. This one I have never done but I have heard it works for other people. If you have a bottom dresser drawer you can clean out do and line it with towels on blankets. Then, move the babies into there and Kaylee should follow. Close the dresser drawer most of the way, leaving enough room for Kaylee to climb in and out. In theory this will be a cozy den and make her feel more comforted.
If that's not an option, I would maybe try for 24 hours just closing her in the closet. For this period, I would minimize checking in on her and let her sort herself out and find out what makes her comfortable. If she's insistent on being in the litterbox, go buy a second one that she can use to go to the bathroom in. Maybe set some blankets and towels around so she has different options of where to nest. If possible, try to find something covered (even a cardboard box turned on it's side with blankets or towels in it may give her the comfort she needs). If you have the money, a covered cat bed from the petstore works really well. This time will be stressful for you, but just commit to 24 hours and see what happens. Really, for her at this point being confined may be best, as it gives her limited options on where to nest. She may be feeling like she has too many choices right now and can't decide what is the best place. She may just need some quiet time to calm down and reestablish her routine. If in that time she doesn't than, as Clynn said, it may be time for you to step in and help with eliminating and supplemental feeding. That said, I am a big fan of trying to let Mom sort it out, because once you intervene there is no going back. It should only be done if absolutely necessary. I spent my first litter terrified and intervening on everything, I calmed down with later litters and realized a lot of the time Mom is capable, I just needed to give her a chance to get there.
I agree with Clynn that the den moves aren't good for her or her babies. My point was rather that in an environment like yours (and mine), where she can't be totally isolated they are more common, and it is up to you to try and give her acceptable places to nest. Hopefully if that happens she will settle down.
Finally, I think you may need to bite the financial bullet and take her in for a vet visit. It doesn't sound to me like anything is wrong with her (but again I am not there so only you know) other than being stressed, but I think you need the reassurance. The vet can look over her and the babies and give you some peace of mind that they are okay, or alternatively, help you solve whatever may be wrong. They may also have some better tips on how to help her settle down.
I hope they are okay. Mommy was doing such a good job in the beginning but she seems to be getting frustrated and confused and doesn't like being locked in the closet but moves around to much if allowed in the whole room.
