Brian, as Cody suggested, it would be good to try and get your snake switched over to pre-killed food. Either freshly killed or frozen/thawed. When you're able to handle him again, check him over carefully for bite marks. If you find that the rat broke the skin, you'll want to treat it with an antibiotic for awhile and make sure it stays clean.

As for the possible burns...Is there anything in the tank that he could burn himself on??? Do you use a hot-rock or have an exposed bulb in his enclosure? If you've had him for this long without noticing any old burns, and there is nothing in his cage that could burn him, then it's likely what you're seeing is either some old shed, or maybe the bites from that rat? Or a previous rat and you didn't notice the bites before? If there IS a source for burns, remove it immediately. Please let us know as soon as you can handle him, what those spots look like.

About the shedding issues: Sounds like you might need to work on the humidity levels a little bit. What do you usually keep them at? Do you increase humidity during a shed? What sort of hygrometer are you using?