This may sound funny but check the Starter. If the brushes are really bad then it won't turn over fast enough under compression to create enough spark to fire the motor.
I had that gremlin under the hood of my wife's sx650 for about a week. I tried every electrical component from mine in hers with no avail. Finally in desperation I thought what the heck the only thing I haven't swapped is the starter. It fired right up.