I take it that the electric shift doesn't work either, does it do anything? Do you hear a noise or anything that indicates that the shift servo is trying to work? Doesn't the shop manual tell you how to read the codes? By shop manual, do you mean the owners manual or do you have an actual repair manual? You need a repair manual, the owners manual isn't good for much more than telling you what kind of oil to put in it. I have no idea what the flash codes mean, but if the machine won't even shift manually, I would guess that either your clutch is faulty, out of adjustment, or you have bent shift forks or some other damage to the gearshift mechanism. I would start at the clutch since it is easier to get to and it can be adjusted from what I understand. The shop manual should tell you how to do it. If that doesn't help you could remove the side cover and inspect the shift ratchet. If it is a bent shift fork, or shift drum problem, you would have to get inside the motor.
Yours truly, sincerelly, love always, Josh aka The DirtDemon.