I have a 95 z440 It has no spark on the pto side, I changed plugs didn't help, so went with the next least expensive part, the coil. That didn't help. The next part is the cdi box. But before I do that I need to know, can the cdi box only fail on one side. I was always told that either it works or it does'nt.
No, is only provides a single spark pulse to the coil and that fires off every 180 degrees.
Go back to the plug wires and check the end caps have good connection to the wires. Unscrew the ends and clip off 1/4" and try again.