Hello JanetFlight,
You are correct, there are two different typres of exhaust cone fitted to the -80C2D1F. The longer one is the older version has now been ammended by the shorter one, however the later variation is more prone to cracking around the hole at the rear! You can still fit either type. At my old company (FedEx) you had to have a matched pair on the No.1 & 3 (wing) engines, i.e both long or both short. It didn't matter what was on the No.2 (tail) engine. There was a note on the engine change workcard to specify this.
However, this doesn't seem to matter anymore. In my latter days at FedEx one MD-11 rolled into the gate (N601FE) with a long & short exhaust cone on each engine. On checking the maintenance manual and engine change workcard the requirement had been revised and you could fit either type to any position. Hope this helps you a little.
Cheers
Flightmech