Paul,
Amongst my own recent discoveries, I learned that the magneto end cover on an ATD-equipped machine holds the magneto cam ring in place and aligned with the stop pin. I don't really know if this is the same for manual advance (and don't know which system you have). If your end cover was loose it does seem possible that the cam ring moved, which could explain timing that caused heavy backfire through the carb.
For your sake, I'm hoping for no serious damage or, worst case, damage limited to the top end, being much easier to deal with than a complete disassemble.
Richard L.