Free roaming adult box training

Question
Last summer I took ownership of my roommate's ferret, Calypso, as he was unable to give her the time and attention she needed, and then was transferred for work, so it was pretty natural for me to keep her.
Almost immediately she underwent a massive personality change  for the positive. She quite literally went from being the most aggressive animal I had ever met, to being extremely affectionate, not minding being held and petted. During that time I think a major part of the change was her activity level helping her personality as she went from being pretty much cage-bound to me expanding her area of roaming. I understand ferrets need to understand their territory pretty specifically, so we started with her being out of her cage in her room while I was at work then I would get home and put her up to rest. Eventually I let her have the run of her room with her cage open but the room door closed. After that she graduated to being allowed to freely roam the main floor of the house, and then finally having free roam of the whole house.
She has proven to be extremely trainable since then, I've been able to easily teach her to let me know when she's tired of playing or wants to be put down if I am holding her by giving a kiss on my cheek rather than biting or squirming. However I continue to struggle with box training her around the house. Ultimately she is good 100 of the time when caged, and only had accidents maybe once or twice when confined to her room. But since being allowed to roam free in the house her misses seem to get more frequent, to where I think she is now only using the box around 60 of the time, and I feels she's capable of better accuracy if i could just figure out how to teach her!

I currently use several cheap aluminum brownie pans (they're only about 1" deep so not difficult for her to back into)around the house, and her litter is Yesterday's News recycled newspaper pellets. I've been using both the method of placing her in the box when she starts backing into a corner, and also rewarding her with a dab of ferretone when she does her business in the right place, but its kind of hit or miss when I'm not with her every second.
I'm worried about the pellets being uncomfortable for her feet (i understand ferret footpads are very sensitive) causing this behavior, but shredded paper isn't an option as that's one of her favorite things to play and nest in. I've wondered about maybe using the hamster bedding that is like hay/alfalfa (no wood chips) but I don't know if that would be bad for ferret respiration.
At this point she is somewhere around 6 years old (though she doesn't seem elderly), so I need to know if at this point i should even be trying to further train her or just let her enjoy herself and not sweat a few accidents.
Thanks for your time!

Answer
Dear Rebecca,

I'm very impressed with the steps you have taken to allow your ferret to free roam, it's the mark of a wonderful ferret owner.

Now onto your questions, but first I have a few questions of my own.

Does she go in the middle of the floor? If so there is more than likely not a whole lot you can do to fix that.

Do you have litter boxes in all the corners? Does she specifically pick the ones without litter boxes in it or is it more of what ever is closer.

I think you are on the right track with rewarding her behavior when she does go in the box but you might want to do it a little differently.

Ferrets like most other animals can be clicker trained. That would help, in my opinion, a lot with reinforcing the idea that she needs to use the litter box all the time.

I would start out by getting a clicker (cheap at most petstores) then take some ferret tone, your ferret and you into a room with little distractions Click the clicker and then immediately give your ferret a quick lick of the treat. (don't give something that will take long to eat, that's why a lick of ferret tone works well) Continue to do this, repeating over and over again until you ferret reacts to the click. That would more than likely be either the head going up or running to you at the sound of a clicker for a treat. Spread this out so that you can make sure your ferret relates the sound of the click to the treat. Wait until he is distracted then click it and see if he notices. If he does you know he has been conditioned.

Once that is done try to catch your ferret (or place them in the litter box) going in the correct place and click the clicker while he is going/as soon as he finishes. Then give him a lick of ferrettone. Clicker training is so much more reliable and animals (ferrets) seem to respond to it very well if done correctly.

Don't be worried about him being too old, it's never to late to shape a behavior. And if you don't want to deal with retraining him then honestly just don't. You can only decide for yourself what you think is best.

But I do think this is the best option if you want to go through with it given that you seem to have done everything else. And who knows, from there you go start doing tricks with your ferret.

Personally I don't think Yesterday's news is too hard on their feet as long as it's just used for the litter box as you do. Carefresh could work fine, dust would not be an issue. I'm not familiar with hay/alfalfa but I doubt it would harm them at all. I also wanted to add that Pine shavings are fine to use for litter, not bedding, just litter for ferrets. They aren't living in it and that works fine, especially since it is a wide open place, all other bed shavings (ceder mostly) can not be used no matter what, but pine is safe (and can help with smell).

But I want to you to keep in mind sometimes ferrets will have trouble adjusting to new litter, they don't recognize it and might refuse to go in it. Not all ferrets mind you but I just waned to you to be aware that it is a possibility if you do decide to change it

I hope this helped a bit and gave you a few ideas you hadn't thought of, but keep me updated! You sound like a wonderful ferret mom and I wish you luck.

Lindsey

PS My Sun Conures name is Calypso also, just made me smile :)