Hi, Anonymous and the usual suspects are:
1. Severely discharged or a damaged battery, should have 12.5 volts or better and be able to pass a load test if necessary.
2. Check battery terminals for damage or corrosion, check the battery cables at "BOTH" ends for loose, corroded, or broken connectors, "INSIDE" and outside the cable harness, perform connector wiggle test and check cables with an ohmmeter if necessary.
3. Spark plugs in bad condition or partially fouled.
4. Spark plug cables in bad condition and leaking check for leakage in the dark.
5. Spark plug gap too close or too wide.
6. Faulty ignition coil, module, and or sensor.
7. Loose, dirty, or corroded ignition module connector at crankcase.
8. Faulty CKP sensor.
9. Intake air leak.
10. Water, dirt, or rust in the fuel system, carburetor and/or filter.
11. Fuel tank vent system plugged or carburetor vent line closed off.
12. Vacuum line from intake manifold to fuel valve is broken, cracked, pinched, or missing.
13. Carburetor controls misadjusted.
14. Damaged carburetor.
15. Incorrect valve timing.
16. Weak or broken valve springs.
17. Damaged intake or exhaust valve.
18. Check for engine trouble codes
For more information about your issue and valuable "FREE" downloads that you will need please click on the links below. Good luck and have nice a day.
1999 Yamaha R1 Flatspot Biker ie Forums
1998 1999 Yamaha YZF R1 Service Manual R1 Moto Data Project
OEM parts for Yamaha