Oh poor baby. I'd venture to say from the patterning that yes, he does look like a box turtle. I have little to no experience with turtles though other than my friend's box turtle.

I'm glad it's coming off his shell, I'm more concerned about his skin though. I think your wooden enclusure is the best bet for him, from the sounds of it. Have you put anything in his belly yet, or found out if he's even interested in food? He deserves a nice salad after what he's been through. Pretty little baby.