On most snowmobiles, a single "double coil" fires BOTH plugs simultaneously. If it will fire one cylinder, the CDI box is working..Sounds more like a bad coil or plug wire...
This place might be able to help..http://www.psep.biz/store/john_deere_snow.htm
This place might be able to help..http://www.psep.biz/store/john_deere_snow.htm