Glad he's healthy, but now I'll be sending Use The ****ing Litterbox vibes!
Will he use puppy pads? Seriously, those saved my life. Rinnie uses the box in the cage if I keep it clean, but when she's running around my room she won't touch the boxes. She will, however, use pads. I buy a little package of about ten pads maybe every month or two. I cut them up (either into halves or sixths, depending on where I'm putting them) and they work wonderfully. I went from having four litterboxes outside the cage (plus pads) and four litterboxes inside the cage (plus pads) to one litterbox in the cage (plus a pad) and one litterbox outside the cage (plus two pads).
I think it also helped that I modified their cage and now just have them in the top section of a FN142 with two shelves instead of one. Not so much extra space to poop all over now!