Motorcycle Questions? Ask a Mechanic.
Hi and thank you for your question.
Yamaha does not provide any tests of checks for the ignitor unit. They address it in a backwards kind of way by saying test everything else and if it is all good, replace the ignitor. This actually works well, but it puts the responsibility of accurately diagnosing the ignition system squarely on you. I assure you more than one mechanic has been disappointed to realize replacing the ignitor unit did not resolve their problems.
If you have swapped the entire coil assembly, including the spark plug cap, and were working with a new or known good spark plug, the problem is somewhere else.
This bike uses a digital ignition so there in only one pick up coil, so obviously that isn't bad. If you are reasonably sure the ignitor you tried is a good unit, the last variable here is the wires between the ignitor and the coils. Check from the connector at the ignitor and the primary side of the ignition coils. You are mainly interested in either the gray wire or the orange wire. You should have battery voltage at the black and red wire to each coil as well anytime the key is on as well.