Unlikely to be crank seals.
Sounds like gunk in the pilot jet.
If it is air ingress, check the cylinder base gasket before you go pulling anything apart.
These bikes have a weakness in the seam of the main chamber of the exhaust which sometimes splits when there is a decent "backfire". If you had said that the exhaust sounded louder I would have suggested checking this out.
If it revved high for a long time before you got it stopped it may have done some damage to the cylinder, piston or rings. You can check for damage by looking up the exhaust port with the pipe off.
Sounds a bit odd that you say it stopped with a backfire when the fuel supply was shut off. It usually takes quite a while to stop an engine just by turning the fuel off.
Next time I suggest you block the exhaust outlet or turn the bike completely upside down to stop a runaway motor.