You could try some more removal since Jody's maindeck is a little light. Otherwise I'm jamming the combo at them as quickly as possible and being very aggressive regarding their manabase. Sparkii's academy ruins list has also been very nice against the 3-drop decks.

What particular counters are you having trouble with? Czech around me is running FoW with maybe a few Daze or Counterspell so it hasn't felt too bad to play through. Leovold's triggers and the crapton of sideboard cards are where I've had trouble personally.