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What you have done so far really for the most part wouldn't affect how the engine would run. Probably a sensor has gone bad and causing the EFI to go faulty. You can install you recoil, it wouldn't affect running whatsoever. First I would take off the injector and clean it. It is probably a O2 sensors or somthing of the sorts. Honda has readings in there manual to test a sensor with a multimeter to test wether its bad or not. I would pull up a diagram and find the location of every sensors and check them after cleaning the injector. You should find your culprit in there. There usually is a airtemp sensor in the airbox, since your engine changes with air temp my guess is that sensor has gone bad.
 

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What are the temperatures they want you to test at? I’ve been able to test sensors by sticking them in a mini convection oven I use for powdercoating/cerakoting with the wires sticking out the door. Do remember that every part you use may not be able to be refunded. Once you use that fuel pump it is deemed hazardous and Amazon will not take it back(in my experience). Have you checked for consistent spark? I’ve seen people get wrapped up over fuel issues not realizing that their spark was intermintant due to a fried coil. Let’s ignore all that though. Your engine if the compression is good shouldn’t be an issue especially if the valves were checked. This leaves your throttle body’s sensors or injector. I am certain it is your IAT sensor. All the other components really wouldn’t affect an idle (in this case your machine barely idles if I’m correct) if the IAT sensor is bad it will affect every other system of the EFI. If it was any of the other sensors your machine would start and idle like a dime every time but the second you give it any sort of throttle all hell breaks loose. In your case hard starting indicates a bad IAT sensor that is telling the ecu to give it way too much fuel. What I like to do to eliminate confusion is disconnect all fuel lines and electrical components and make sure that it still sparks well when this happens. Then shoot a little gas down the throat and bottle feed it. This lets me know it’s the fuel system. You could try unplugging the IAT sensor and seeing if it changes. Really anything that make the machine respond will point you in the right direction. Good luck.
 

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ECUs respond differently. There’s no harm in trying since if the ecu responds by leaning out the mixture then you’ll confirm that the issue is that sensor. Usually the machine will try to work without the sensor but it’s not possible for it to run well. If it were working then it would probably die on the spot. In cases like these the atvs ecu isn’t very advanced you can unplug things one at a time and if you get lucky and there is a positive response then that sensor is probably the culprit. Kind of similar to how people test coils on a car. I’ve had some luck with it but again it’s not full proof. I’m more then certain it’s not the fuel pump though. The only issue you can get with them is weak pressure, since your machine changes how it acts with temperature it kind of eliminates that factor. Gasoline dosen’t get harder or easier to pump with temperature. If you want to eliminate the pump factor just make sure it pumps into a cup and if all else fails replace it if you couldn’t have gotten a tester on it but it’s a rare day to see a pump go on atv. I’d recommend testing a handful of sensors your can get to easily. First take them and read them even though the temp isn’t optimal, if there is one that is very off you found it. You can also just bring them into your house and let it sit for a day and test them. When I used to test electrical components temperature really didn’t matter unless it was too a extreme (low 10 or high 100) even then it would barely affect the reading. Again what you could try is just blocking off the fuel rail and for safety unplugging the injector, making sure it still sparks and then getting it to run off starting fluid or gas in a squirt bottle. If it fires off and you can get it to rev then it means your issue is a sensor in the throttle body. Remeber that without the fuel to the injector, the efi is basically deemed useless and by shooting fuel down the throat your doing what a carbeurator would and your now the only source for fuel. The engine could care less aslong as it gets gas and the ecu dosent cut the spark if one of the connectors isn’t plugged in. I use this method a lot in diagnosis so you could give it a try if you want, can’t really harm anything. The more you find out about the issue, the faster you can fix it when parts roll in.
Edit: If you want to try what I said you probably only need to unplug the injector rather than blocking off the fuel. Pretty easy trial.
 
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