I would do 1, then 3 if it where me.
If I understood right, it was running fine before the TORS disconnect, then you fired it up and it was backfiring (but didn't ride it).
You're not usually gonna do much damage to a motor if it was just idling or revving in neutral (UNLESS, as Starwriter mentioned, you put straight gas in it). The timing plate could have come loose (which would cause the backfire), or something on the clutch side.