Here's a thread that can help you figure out how to get a glass tank working well:
http://www.ball-pythons.net/forums/s...ad.php?t=56846
My only problem with replacing the aspen with paper in the glass tank is that you apparently have an unregulated heat mat under the glass. The paper will not protect him from that. I'm just guessing this, since you seem to think it likely that the snake has been burned.
If living in a chilly basement...see if you can get even just one corner of a room warmed up with a space heater. They make some pretty nice ones now that don't cost a lot and have a built in thermostat so you can control (at least to some degree, even if not completely accurate) how warm that corner gets. And you can cover the glass with insulation to help hold in warmth as well.
The heat mat, or whatever it was that burned him, needs to be turned off. If you have no other options for warming the tank...then get to the hardware store asap and pick up a rheostat. (Dimmer switch) They make them for table lamps that you just plug into like an extension cord. The mats get TOO hot without something to control them.
It's unlikely that substrate that has been spritzed for humidity would cause scale rot...but if it's been left soaking wet and/or not cleaned for a long time...it's possible. And it's possible that it's a combination of burned scales that have gotten infected by laying on dirty or wet bedding.
Even if I saw pictures, I wouldn't hazzard a guess as to what the snake's actual condition was. I'm just trying to offer some basic ideas to help keep whatever it is from getting worse until it can be treated by a knowlegeable vet.