The Atv was sparking fine until we had to take off the flywheel. I researched how to put it back on correctly and I think I did. It sparks when I push start it but not with the electric start. Does it have anything to do with the fly wheel? Any ideas.

 

That problem is common on CDI ignition systems and nobody seems to have an answer. However some recon it is the pick up coil dirty, so I wonder if you have knocked the pick up coil when you put the flywheel back, and altered the air gap between it and the flywheel. On some Yams there is a wire from the neutral switch to CDI, I assume to increase the spark for starting, if this is disconnected it will give those symptoms.

 

I will look into that thanks. Is there a way that you can test the CDI

 

No, and if it sparks at all it is unlikely to be the CDI.