When mine was flaking out it would run on 3 cylinders some of the time, occasionally run just fine and occasionally just freaking die completely on the side of the road.
It was very intermittent and a pain in the ass to troubleshoot.
The service manual, available over at Vmax outlaw has a very simple troubleshooting procedure to check the coils and pickups. It basically says if the coils and pickups are checking out good to replace the TCI (ignitor)
I recommend the Dyna 3000, others don't like them but I've got close to 20,000 on my with no problems, an adjustable advance curve and a rev-limiter to boot.
It's also much cheaper than a new yamaha TCI, sometimes used yamaha ignitors can be found on Ebay for cheap.
Rusty.