ok so i have a 2013 raptor 700. beast of a machine,,,,has the big 3 done..that being intake big gun true duals and a junk big gun programmer...i wrecked pretty damn hard one day and broke the sub frame so i put the poor girl away for a couple months till i got around to fixing it. got it all fixed up with a new sub frame and a few other things i messed up.of course by this time the battery was dead which was no surprise because it wasn't super great before i wrecked but when jump started it ran great! got tired of jump starting it so i went out and bought a new battery. hooked it up and somehow now i have some sort of massive fueling issue..not sure if its a coincidence or if i messed it up. basically its just throwing raw fuel into the cylinder at an alarming rate. not even joking i can waste a gallon of gas on the floor out the exhaust in a minute of cranking. thought it was a stuck injector so i held it in the rail while i turned the key on for the pump to run. sprayed like crazy so i unplugged it to confirm my theory of a stuck injector and it stopped as well so the injector was not stuck, something was telling it to dump fuel as long as the pump was on..next test i went to the tps...ohmed out a little wacky so i replaced and adjusted it as correctly as i could without it running right. if i remove the fuel from the tank it will run and idle (like crap) but the second i put more fuel in the tank its as if i opened up the flood gates and the bike will no longer start just proceed to spew my money on the floor in a ridiculous amount...i guess my reason for the forum is to find out what module or sensor tell the injector its duty cycle or fuel rate? ecu? Please make note the bike internals are stock and the tuner is completely removed from the bike...please someone help i want to rip on my rappy again.

 

Don't know if this helps you or not.

The central component of the system is the ECU which manages system operation, determining the best combination of fuel mixture and ignition timing for the current operating conditions. An in-tank electric fuel pump is used to move fuel from the tank through the fuel line and in-line fuel filter. The in-tank fuel pressure regulator maintains a constant system operating pressure and returns any excess fuel to the tank. At the engine, fuel is fed through the fuel rail and into the injectors, which protrude into the intake ports. The ECU controls the amount of fuel fed to the engine by varying the length of time that the injectors are energized. The controlled injection of the fuel occurs on each crankshaft revolution, or twice for each 4-stroke cycle. One-half the total amount of fuel needed for one firing of a cylinder is injected during each revolution. When the intake valve opens, the fuel/air mixture is drawn into the combustion chamber, ignited, and burned.

The ECU controls the amount of fuel being injected and the ignition timing by monitoring the primary sensor signals for air temperature, barometric air pressure, engine temperature, engine speed (RPM), and throttle position (load). These primary signals are compared to the programming in the ECU computer chip, and the ECU adjusts the fuel delivery and ignition timing to match the values.

The ECU has the ability to compensate on-the-fly for changes in overall engine condition and operating environment. This allows it to maintain the ideal air/fuel ratio regardless of temperature, demand, or altitude.

During certain operating periods such as cold starts, warm up, acceleration, etc., a richer air/fuel ratio is automatically calculated by the ECU.

 

Can't help with the ECU issue, but if it runs without fuel, the sump must be full of fuel from the overfueling issue, that is the only place it can have come from. Our local Yam dealer is good at after sales service, so we don't get Yams in to repair much, and Yamaha were about the last firm to go EFI so I haven't had to work on their EFI systems, but Honda & Suzuki both give fault codes on the dash if something electronic goes wrong with the fuel system. Must be worth getting your local Yam dealer to take a look with his diagnostic tools.

 

I'm an auto tech and their injector are controlled by the ECU. Should be the same for the Raptor. The injector has constant 12v when the key is on, the ECU supplies the ground to control the pulse.
You have a ground problem. Might be internal in the ECU or the wire between the ECU and injector.