There is a little black box under the gas tank you can find it by tracing the wires on the clutch cable to it. Disconnect the wires and see what happens. Yamaha has had a lot of trouble with this component it works as a safety and when it goes bad the bike will only fire on one cylinder.
Previously owned bikes:81-yz80,82-ty80, 85-tri moto 200, 84-rm125, 85 xr200, 84 rm500, 87 rm125, 83 honda big red, 88-250r, 89-250 quadracer, 90- 500 quadzilla,86 cr500, 91-250 quadracer, 86 tri-z, 89 xt600, 94 fzr600, 95 timberwolf, 93-banshee, 88- 265R, 01-250ex(wifes). 2001 400ex, 440 kit, 03 ds650, 00 big bear 4X4, 01,xr200r, 1995 wr250z, 2002 yz250 2smoker, 2002 husky wr360, 2004 400ex