I'm glad you started this thread i'm having the same problem with my 2003 Kodiak 450. Mine seems moisture related any dew in the morning on my machine it won't start until it dry's out,i just ordered an ignition switch.Lets hope you get some answers.
Only thing I can suggest is to check the safety start switches. There is a neutral start switch and also one that works in conjunction with the brake I believe. Either of those will stop the spark. You might disconnect the ground wire to the coil pack and see if the spark comes back.