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Recently purchased a 2003 R1 w/power commander 3. I was told the bike had sat for a few years. I replaced fuel pump and drained fuel changed oil etc. only to find out I also had no spark. I followed the troubleshooting manual and got no where. Here is where I am a little confused. I am getting over 12 volts at the head of the harness on the hot wire when the key is on and kill switch is on. I was under the impression the second wire is a ground wire? But if I connect a light probe tester to the positive on battery and to the second wire I get nothing doesn’t matter if bike is cranking or etc. I also get no volts or anything coming from the wire either. I check tolerances on the coil packs and they are right in the middle of the range. I insert the spark plug into the boot and ground the plug out and I get nothing when cranking on any of the coil packs. Could anyone clarify to me what the second wire is? I thought it was a ground but the plug is also grounded to the engine when threaded so I’m not sure. Appreciate any help. *spark plugs are brand new*
 

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Recently purchased a 2003 R1 w/power commander 3. I was told the bike had sat for a few years. I replaced fuel pump and drained fuel changed oil etc. only to find out I also had no spark. I followed the troubleshooting manual and got no where. Here is where I am a little confused. I am getting over 12 volts at the head of the harness on the hot wire when the key is on and kill switch is on. I was under the impression the second wire is a ground wire? But if I connect a light probe tester to the positive on battery and to the second wire I get nothing doesn’t matter if bike is cranking or etc. I also get no volts or anything coming from the wire either. I check tolerances on the coil packs and they are right in the middle of the range. I insert the spark plug into the boot and ground the plug out and I get nothing when cranking on any of the coil packs. Could anyone clarify to me what the second wire is? I thought it was a ground but the plug is also grounded to the engine when threaded so I’m not sure. Appreciate any help. *spark plugs are brand new*
I could help if you have a link to a wiring diagram or can post a pic of it.
 

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So i looked into some wiring diagrams and found it is a ground, it’s the solid orange wire on one of the cylinders but the ground is different on each one. I guess it’s an intermittent ground which cuts in and out causing the spark but is controlled by the CDI/igniter. I’m am not getting this ground signal from my CDI and I cannot figure out why. I just tried swapping in a new CDI with no luck. The Crank POS sensor tested good on the ohm test per manual. What other inputs should I be checking? I am going to try cylinder ID and Cam pos. next I guess. I’ll send a picture of the diagram I have though. Thank for the help.
 

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Recently purchased a 2003 R1 w/power commander 3. I was told the bike had sat for a few years. I replaced fuel pump and drained fuel changed oil etc. only to find out I also had no spark. I followed the troubleshooting manual and got no where. Here is where I am a little confused. I am getting over 12 volts at the head of the harness on the hot wire when the key is on and kill switch is on. I was under the impression the second wire is a ground wire? But if I connect a light probe tester to the positive on battery and to the second wire I get nothing doesn’t matter if bike is cranking or etc. I also get no volts or anything coming from the wire either. I check tolerances on the coil packs and they are right in the middle of the range. I insert the spark plug into the boot and ground the plug out and I get nothing when cranking on any of the coil packs. Could anyone clarify to me what the second wire is? I thought it was a ground but the plug is also grounded to the engine when threaded so I’m not sure. Appreciate any help. *spark plugs are brand new*
I could help if you have a link to a wiring diagram or can post a pic of it.

Pic should be up
 

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I guess I can’t post a picture so here is the link to manual https://www.manualslib.com/manual/806496/Yamaha-Yzf-R1p.html?page=389#manual. It’s on page 389
Sorry but that thing is virtually unreadable.
One idea I got from the parts list is the lean angle sensor. Try checking/bypassing that. That most likely cuts the ignition if bad.
So I’m getting spark now on all 4 coils consistently, so I put everything back together and tried to start and it just cranks and cranks like before. So I double checked work again and it was good so I started looking into the fuel, I pulled the injectors and cleaned them and they are all working good. I have a new all balls racing fuel pump in the tank now and I’m wondering if maybe I’m not getting enough pressure. I turned the key with the line off the gas tank and fuel will spray out a few feet but if I cover it with my thumb I can stop any from coming out no problem. So I’m wondering if maybe it’s not building enough pressure? The injectors are getting power and they were working good. If I try to crank the bike and pull the throttle back it sounds like the bike Boggs down and is harder to crank.If I give it a quick spray of starter fluid it will ignite for a second. So surely it’s not getting fuel.
 

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So I’m getting spark now on all 4 coils consistently, so I put everything back together and tried to start and it just cranks and cranks like before. So I double checked work again and it was good so I started looking into the fuel, I pulled the injectors and cleaned them and they are all working good. I have a new all balls racing fuel pump in the tank now and I’m wondering if maybe I’m not getting enough pressure. I turned the key with the line off the gas tank and fuel will spray out a few feet but if I cover it with my thumb I can stop any from coming out no problem. So I’m wondering if maybe it’s not building enough pressure? The injectors are getting power and they were working good. If I try to crank the bike and pull the throttle back it sounds like the bike Boggs down and is harder to crank.If I give it a quick spray of starter fluid it will ignite for a second. So surely it’s not getting fuel.
Yep, it it runs on starter or carb cleaner fluid it's fuel.
Is that pump the correct one?The closest thing to a bike with fuel injection I've worked on was a RZR 800. It was fuel injected and it needed 50psi. Every car I've worked on with port injection needs 60, even TBI injection was 30 psi.

Does the book show what the pressure should be? EDIT: found it, says 40 psi, you better check it.
 
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