ECU fuel pump issue

fossilrider! · Nov 24, 2024

Hi guys/gals, Steve here in Tn.. I'll try to make this as short/painless as I can. I have a '07 FJR1300 manual trans that developed an issue over a year-and-a-half ago. The reason I am just now getting back on the problem is that I had bypass surgery about the time this issue started, so I've been sidelined since then. The issue is that the fuel pump stopped getting power. So, I pulled the tank and seat, and some of the fairing off and started to search. Fuses are all good, all connections that I have checked are good and clean (bike has always been kept inside). Fuel pump relay is good, but I put a new one in anyway. Checked all the ground "spiders" that I could find. I did all this when the issue started and the bike has been sitting since then. So.... I decided a few weeks ago to just bite the bullet and take it to the dealer, where I have known the owners for decades. When they finally got around to checking it out, the tech called and asked me where the ECU was.? I assumed it was on the bike and don't remember removing it. But after it being 1 1/2 years since I worked on it, who knows? Anyway, after looking all over my shop I remembered that a previous owner had installed a "Power Commander", which I had removed during all the digging I had done. Now, since this is the first time I have ever even seen a Power Commander, I started to wonder how they work. Does a Power Commander actually take the place of the OEM ECU or is it simply an add-on? The little I know about these units is that they just allow access into the system so the settings can be tweaked for more power/better fueling, etc.. In that case, the original ECU would stay in place instead of being replaced by the Power Commander.? If this unit replaces the ECU, I can stop looking for the ECU and just take the Power Commander to the shop. Anyway, I'm sure the folk here can lead me in the right direction. Thanks for any info.

Dan Cooper · Nov 24, 2024

fossilrider! said:
Hi guys/gals, Steve here in Tn.. I'll try to make this as short/painless as I can. I have a '07 FJR1300 manual trans that developed an issue over a year-and-a-half ago. The reason I am just now getting back on the problem is that I had bypass surgery about the time this issue started, so I've been sidelined since then. The issue is that the fuel pump stopped getting power. So, I pulled the tank and seat, and some of the fairing off and started to search. Fuses are all good, all connections that I have checked are good and clean (bike has always been kept inside). Fuel pump relay is good, but I put a new one in anyway. Checked all the ground "spiders" that I could find. I did all this when the issue started and the bike has been sitting since then. So.... I decided a few weeks ago to just bite the bullet and take it to the dealer, where I have known the owners for decades. When they finally got around to checking it out, the tech called and asked me where the ECU was.? I assumed it was on the bike and don't remember removing it. But after it being 1 1/2 years since I worked on it, who knows? Anyway, after looking all over my shop I remembered that a previous owner had installed a "Power Commander", which I had removed during all the digging I had done. Now, since this is the first time I have ever even seen a Power Commander, I started to wonder how they work. Does a Power Commander actually take the place of the OEM ECU or is it simply an add-on? The little I know about these units is that they just allow access into the system so the settings can be tweaked for more power/better fueling, etc.. In that case, the original ECU would stay in place instead of being replaced by the Power Commander.? If this unit replaces the ECU, I can stop looking for the ECU and just take the Power Commander to the shop. Anyway, I'm sure the folk here can lead me in the right direction. Thanks for any info.

First, welcome to the circus.
Sorry to hear of your health and scooter problems.

Realizing that time and distractions can cloud one's memory.
Do you remember where the Power Commander was located on the scooter and where the wiring connections were made when you removed it?

The ECU on Gen 2 FJRs is mounted underneath the bottom of the tool tray below the driver's seat.
There is one large connector on the wiring harness that plugs onto the ECU.
Remove the side panel on the left below the driver's seat and the cover over the airbox intake to see the ECU and its wiring harness connector.
The ECU will look like this.
https://www.ebay.com/itm/364979454814?_skw=fjr&itmmeta=01JDFNJDQPXCV9PC5BS0NWK85W&hash=item54fa78835e:g:1fUAAOSwyBFmgKy4&itmprp=enc:AQAJAAAA4HoV3kP08IDx+KZ9MfhVJKmnuAvMFaGgLEIqQcJcMfCEmsRQWANkIFp3IwPefBmPdkgUE+yZAHW1DeaK7UhIe6NwEb9ZOfyseaHVsoYukNt3qQUNk1v3Y1gKiYNJbNOiqunBR/3H688mdpN6XMce2XbIeTE7Hz01UBlcNjHsL2YzJyKj2+Ph6rftpJArO3AxZQIlvB80rEd4farX5wBQibA+edxIXcSD4fqcM544NYSBf2LfmC1kyoboS591H56Jlw26PZqs1tQNYfZkn4V5to0QNLy8aIMeW/AiC7BPYquh|tkp:Bk9SR_rbyfXrZA
You would probably remember if the ECU was removed since there is some associated disassembly of the tool tray to get to the mounting screws.

If the original ECU is lost or not found this ECU would make a good replacement. If you should have to buy a replacement ECU, one from 2008 - 2012 would be a good choice since it improves some of the fueling issues from the 2006 - 2007 ECUs.

This is not my ECU, and I have no association with the vendor or previous owner.

dan

Dan Cooper · Nov 24, 2024

A couple of other things I didn't touch on earlier.
When you turn on the key does the dash light up and the gauges make a full cycle sweep?
When you press the start button does the engine spin with authority?
Is the Kill Switch in the Run position?
Are you sure you have a known good battery?

If I remember correctly, and I may not, I think there was a recall for the ignition switch on those models. Has that recall been done? Entering your VIN on the Yamaha website will tell you if recalls have been completed or ask the dealer mechanic to check.
There was also a recall for the S4 ground spider wiring modification.

dan

RossKean · Nov 24, 2024

The PC III connects in-line and does NOT replace the ECU. There is no reason why you would remove the ECU. If you disconnected the PC III and didn't reconnect the injectors then the bike wouldn't run. The attached file is the installation instructions for the Power Commander III USB.

Full information here:
https://www.dynojet.com/power-commander-iii-usb-for-2006-2008-yamaha-fjr-1300-419-411/

fossilrider! · Nov 24, 2024

Wow, thanks guys. New battery. Kill switch in on position. When I was working with it (1 1/2 year ago) the engine spun great, and the gauges did a full sweep, but the fuel pump never made an attempt to turn on. The pump would not energize before I took anything apart, that's what started this whole ordeal. When the tech called me about the ECU, he did say there was a recall on a part of the ground wiring but the part (sub-harness?) is on back order. I bought a shop manual and traced the wiring as best I could and, if I remember correctly, I found that a yellow/black wire ran from the relay back toward the pump but it went into the harness and I couldn't see where it ever came out and made it to the pump. About that time is when I got derailed. I take it that the later '08-'12 ECU is a plug and play on the '07.? I see some on ebay that some are listed as '06-'12. I take it there is a different part# for the '06-'07 and the '08-'12.? I will get back to my shop again tomorrow and search some more, but I think if I removed it (which I obviously did) it should be right in the area where the bike and all other removed parts have been sitting for over a year. Very puzzling.? Also, the tank, seat, heat shield (under the tank) tray under the seat, and side fairing and lowers are still off. I told the tech that I just needed him to get the pump working and I can put it all back together. Thanks again for the input and info.

Dan Cooper · Nov 24, 2024

fossilrider! said:
Wow, thanks guys. New battery. Kill switch in on position. When I was working with it (1 1/2 year ago) the engine spun great, and the gauges did a full sweep, but the fuel pump never made an attempt to turn on. The pump would not energize before I took anything apart, that's what started this whole ordeal. When the tech called me about the ECU, he did say there was a recall on a part of the ground wiring but the part (sub-harness?) is on back order. I bought a shop manual and traced the wiring as best I could and, if I remember correctly, I found that a yellow/black wire ran from the relay back toward the pump but it went into the harness and I couldn't see where it ever came out and made it to the pump. About that time is when I got derailed. I take it that the later '08-'12 ECU is a plug and play on the '07.? I see some on ebay that some are listed as '06-'12. I take it there is a different part# for the '06-'07 and the '08-'12.? I will get back to my shop again tomorrow and search some more, but I think if I removed it (which I obviously did) it should be right in the area where the bike and all other removed parts have been sitting for over a year. Very puzzling.? Also, the tank, seat, heat shield (under the tank) tray under the seat, and side fairing and lowers are still off. I told the tech that I just needed him to get the pump working and I can put it all back together. Thanks again for the input and info.

Yes, all Gen 2 ECUs are interchangeable plug n' play. The early Gen 2 ECUs (2006 - 2007) were throttle finicky with somewhat lean fueling maps, which is why some added the Power Commanders. The later Gen 2 ECUs (2008 - 2012)(and especially 2010 - 2012) have better suited fuel maps and may negate the need for the PCs.
Many of the E-Bay vendors are not knowledgeable about the specifics of every part on every scooter for every year of a model run. They list many parts incorrectly for some generations of scooters lumping all years together. Be sure to check the details of the listings about the specific year model a part was removed from and if no specific year is listed, just move on to the next listing.

If the tool tray under the seat is in your shop, the ECU is very likely still attached to the bottom side of it.
The service tech will most likely need the ECU to get the fuel pump running.
If the tank is in your shop, how is the service tech supposed to get the fuel pump running?

Incidentally the fuel pump ground path is through the S3 ground spider and subsequently through the "Dreaded" S4 ground spider. If either of those spiders are damaged / burned there will be problems with the fuel pump and possibly the fuel gauge. There may be other functions impacted further upstream from S4.

dan

torch · Nov 25, 2024

Dan Cooper said:
Yes, all Gen 2 ECUs are interchangeable plug n' play.

Not all, USA only. Canadian and European ECUs are married to the immobilizer system installed on the bike. Make sure you get a US ECU if you are shopping.

SkooterG · Nov 25, 2024

torch said:
Not all, USA only. Canadian and European ECUs are married to the immobilizer system installed on the bike. Make sure you get a US ECU if you are shopping.

I am also wondering if the ECUs are different between the 'A' and 'AE' (Auto clutch) models?

SkooterG · Nov 25, 2024

Dan Cooper said:
The early Gen 2 ECUs (2006 - 2007) were throttle finicky with somewhat lean fueling maps, which is why some added the Power Commanders.

I think most of the 'throttle finickiness' came from the poorly designed throttle cam shape on the '06 and '07. Not that fueling maps were improved over the years.

RossKean · Nov 25, 2024

SkooterG said:
I think most of the 'throttle finickiness' came from the poorly designed throttle cam shape on the '06 and '07. Not that fueling maps were improved over the years.

I think a little of each - seems to me that replacement of the throttle tube with the G2 (different profile) helped some a bit (I realize that the weird cam shape was on the throttle body end). I had a PC III on my '07 but took it off as it killed fuel economy - got used to the throttle after a bit of time. I think the Ivan flash has done good things for some owners of early Gen II bikes.

Dan Cooper · Nov 25, 2024

SkooterG said:
I think most of the 'throttle finickiness' came from the poorly designed throttle cam shape on the '06 and '07. Not that fueling maps were improved over the years.

SkooterG said:
I am also wondering if the ECUs are different between the 'A' and 'AE' (Auto clutch) models?

The 2006 - 2007 throttle finickiness was a combination of the throttle cam and ECU fuel mapping.
The throttle cam profile made the low end opening too abrupt, and the fuel maps were too lean with a couple of sharp steps just off idle.

Had a 2008 "AE" model that exhibited some running issues when hot. Wasn't sure if the problem was throttle body or fuel pump or ECU related.
It was cheapest and easiest to replace the ECU with a 2010 "A" model ECU that I found at a great price at the time.
The 2010 ECU solved the running issues and as a bonus the scooter ran smoother than ever and got better fuel mileage.
Not sure just what the failure was with the "old" ECU, quit looking when the problems went away.

When looking at the parts fiche, the "A" and "AE" ECUs carry the same part numbers for any given year.

dan

YMMV

fossilrider! · Nov 25, 2024

Once again, thanks guys. The tank went with the bike to the dealer. I am heading to my shop (about 15 miles from home) to have another look. My shop is FULL of bikes, parts, tools, equipment, and a Chevy truck (all apart), but I try to at least keep parts in the same area as the project.

CCook82 · Nov 25, 2024

RossKean said:
I think a little of each - seems to me that replacement of the throttle tube with the G2 (different profile) helped some a bit (I realize that the weird cam shape was on the throttle body end). I had a PC III on my '07 but took it off as it killed fuel economy - got used to the throttle after a bit of time. I think the Ivan flash has done good things for some owners of early Gen II bikes.

My experience also. G2 Throttle tube would have or did have for me maybe a 40% favorable effect but that was not enough for smooth roll on or offs. The PC III provided the remaining smooth out for that.

dcarver · Nov 25, 2024

I think most of the 'throttle finickiness' came from the poorly designed throttle cam shape on the '06 and '07. Not that fueling maps were improved over the years.

Had my 06 ECU reflashed by Ivan. He said 06 ECU's had minimal RAM for mapping details. Later ECU's, compatible with the 06, had waaay more memory to allow more precise mapping. I sent him the 06 OEM, he sent back a re-flashed unit with more RAM and holy crap Batman, huge difference! Not so much of a difference on the 2013.. but on the gen 2 2006.. Wowzers. Worth every penny and I'm frugal as Skooter$G.
Clicky

Ivan's Reflash Info Here

fossilrider! · Nov 26, 2024

FOUND IT ! I went back to my shop and began to pull together an look at everything I had pulled off the bike and there it was, right where one of you said, under the tool tray. What a relief. I will take it to the dealer here in a little while and talk with the tech to see if he has any idea about the time frame on the back ordered part. I would be tempted to get the later '08-'12 ECU anyway, and might still do that if I keep the bike. I just haven't been riding much at all in the last few years and am letting some of the bikes go. Just sole a '76 Guzzi and have a couple others that will probably be going. I have been in 46 states on a bike, but because of life getting in the way the bikes mostly just sit. I know, a pity! Thanks again for the help, guys. Ride safe.... and as often as you can.

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