Hi, Anonymous and the usual suspects are:
1. Fuel tank empty.
2. Fuel supply valve/petcock turned off.
3. Fouled spark plugs.
4. Engine flooded as a result of overuse of the enricher.
5. Vacuum hose to the fuel supply valve/petcock disconnected, broken, cracked, or pinched.
6. Fuel valve/petcock or filter clogged.
7. Fuel line to carburetor or throttle body pinched or kinked.
8. Carburetor float stuck.
9. Fuel injectors clogged.
10. Severely discharged or damaged battery, you need 12.5 volts or better and be able to pass a load test if necessary.
11. 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.
12. Loose or corroded wire connection at the coil, battery or plug between ignition sensor and CDI box.
Spark plug cables in bad condition and shorting check for leakage in the dark, cable connections loose, or connected to the wrong cylinders.
13. Ignition timing incorrect due to a faulty MAP, CKP, O2, TPS, sensors.
14. Faulty neutral, clutch lever, or kickstand safety switch.
15. Faulty fuel pump or fuse or relay.
16. Faulty CDI box.
17. A stuck bent or burnt valve.
18. Tip over sensor needs a reset.
19. 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 a nice day.
Yamaha XJR1300 99 Service Manual
OEM parts for Yamaha
YAMAHA XJR1300 Owner Manual
Btw, I’m available to help over the phone in case u need at https://www.6ya.com/expert/gregg_c0ec1df182c7330e