Check your pulser, white/red wire and white/blue wire, should have 459-561 ohms between them.
then the rotor rotation direction sensing coil, red wire and white/blue wires, should have .085-.105 ohms.
If those check good then maybe I'd start thinking CDI, but it's rare that these later model CDI's go out for no reason.
just for kicks try unplugging the rectifier and see if it makes a difference. An RTA at yamaha showed me that trick on a Raptor once but couldn't explain why it made the unit fire, but it did. Seems like it was the rotor direction coil. The rotor direction coil is supposed to keep the machine from misfiring and shearing off the starter bearing bolts.