Def dont get it fixed by yamaha. They just want your money. You can find a used one in the for sale section right here on the site.
There is a way to test the cdi. I just dont know how to do it. You might need 2 people. One to crank while one holds the circuit tester.
Also try swapping the plug wires. see if it happens in the other cylinder when switched.
Hope this helps some.