I would start from the carb and work my way to the cylinder heads by removing the manifold in an attempt to find the missing nut. Remove the exhaust and look into the exhaust valve ports with a small bright light through the spark plug holes. If you can determine which cylinder it's in, you may have to remove the affected head to get at things.

You could also remove the spark plugs and turn the engine over with a wrench to see if it will still turn without "feeling" damage.

If it is lodged in a valve, try to determine if in the valve seat area BEFORE you remove it. If yes, you may need a seat re-grind or replacement of the head.

If it went into the cylinder, it may have punched a hole through the piston head and/or damaged the cylinder head, since they are aluminum and there is little clearance in a number of spots where those two come close together.

Start looking...