Earthquake-Gastrodon is a surefire counter to Sub-CM Jirachi. Gliscor is less of a counter, but will still deal a lot of damage with Earthquake. Outside of rain, Volcanora might try to setup along you.
Dragons aren't the best answer, as Gastrodon might carry Ice Beam. Try Celebi, it survives any Gastrodon and (not-acrobat-)Gliscor. For Volcanora, just run rain and SR, otherwise Terrakion is pretty solid.
Depending on which moves you run, there are a few more counters. Thunderbolt is a must, run Psyshock and Tyranitar kills you, run Flash Cannon and you will loose any CM war agaist those with Recovery (Latias, Reuniclus). A good answer to Tyranitar is Terrakion or Lucario, Scizor is good against Reuniclus and Latias.