Duncan,
That could be caused by anything. Check the obvious electrical items like you mentioned. Cracked spark plug, loose coil and or leads. Check both coils/wires/plugs for spark by pulling them, grounding the plugs to the engine then looking at the plugs when then engine is turning over.
Also check the intake rubbers closely to see if any are cracked especially under the clamps. While you are at it check the vacuum caps also. A bad vacuum leak could cause backfiring like you mentioned.
How long was the bike in storage? Did you add fuel stabilizer when parked? If it was a long time, you could have some gelled fuel in a carb messing things up.
Grasping at straws here.
