Your kitten is still young, she needs more litter pans, they need to be together, not on different floors. You are asking her to do something she is not able to do, which is hold her bowels until she gets to the box. Make more boxes available for her, and as Renae said, use those disposable cake pans and aluminum foil trays. Cats do not by instinct pee and poop in the same place, so again, she needs two pans in the same place- you should give her these pans both upstairs and downstairs.
You come here to get help and advice and this is what we are doing, trying to help you with this kitten. Do not dismiss what is said here by giving up excuses to explain your behavior. Although your intentions were good, you are doing the wrong thing with this kitten right now, and you need to start doing the right thing.