Does your neutral light work properly?
What you have done (with the described jumpering) is bypass the starting enable circuit - the yellow/black should only be at 12V when the CDI sees the neutral switch at ground or the clutch switch at ground. So, perhaps, the CDI is not seeing these.
Unfortunately, the jumpering that you did often destroys the output transistor in the CDI for the yellow/black circuit... so even IF the neutral circuit is working, the yellow/black will often no longer be energized, now that you've shorted it to 12V.
DO NOT arbitrarily short across CDI signals unless you truly know what you're doing.
SO, if you have damaged this transistor, your choice is now twofold - replace the CDI OR make a wiring mod that will bypass the CDI's start enable and instead use the clutch switch to provide 12V to the relay - are you game? If so, I'll give you a link to the simple wiring mod to enable the starter when pulling the clutch switch (to bypass a blown CDI transistor).