You'll need to use an enzyme spray to kill the smell entirely (as I'm sure you're aware that just because you can't smell it doesn't mean they can't). Always pre-test this on a fabric sample if using on a rug, as some of them have been known to discolor.
Other important aspects:
As the kitten is a "he," is he fixed? If he is not fixed, he has the urge to mark. It is a possibility he is trying to cover the ferret smell for his own smell as he is trying to be dominant. If he is not fixed, get him fixed.
Make sure the ferret cage is clean, because he still may be trying to put his smell over theirs, especially if there is unclean boxes in the ferret cage (since I assume he can't get into it)
If you can't afford an enzyme spray (I think they're usually around 10$ - here anyway) White vinegar (distilled) also does essentially the same thing, but it makes things reek for some hours before they air out. I had to do this in a bay window that my problem cat tried to deem was her own. It did kill the smell but the entire room was quite rank until it aired out.
EDIT: Last thought. When you had the litter box under the cage and the cat was using it, did the ferrets also keep using it? Or did the cat's use deter the ferrets? I would think, if no one had accidents if the box was there, then perhaps putting it back is the easiest of all of the options - as long as it doesn't promote any of them to go other places.
<message edited by Seelen on Saturday, October 18, 2014 1:36 PM>