Fuel Injector light blinking codes

I doubt the ECU was affected; it just knows what signal it receives, not that any signal irregularity would affect what it's programmed to do. Mine was fine (still throws the knock sensor code above 4k but that's a different issue I'm still trying to run down without replacing the ECU to eliminate) after the sub-harness replacement. You are correct, I didn't pull anything on the engine, just threaded it through. I would check every injector sub harness connection, looking for bent pins, etc on the male sides and debris inside the female side to see if perhaps something went awry when you replaced the connectors first, starting w/ #2 and the main plug going back to the rest of the harness after verifying they're all connected to the correct cylinders.

Not sure with the fuel ref the injector and how susceptible they are to fouling; maybe run some cleaner (Seafoam, etc) through a small amt of fuel first to see if you can get it to clear all of them out after sitting so long. I just went through gummed up carb orifices on my son's Kawi after letting it sit too long w/ ethanol fuel in it, but haven't ever worried about my ST (I put stabilizer in it and left it sit for a year in FL, started it up and ran out the tank as soon as possible before refilling it with fresh and never had a problem.)

I'm sure others will weigh in if there are any errors in what I've mentioned above; ppl are pretty good at catching the details for us here! Just try to be as deliberate as possible on the troubleshooting so you can eliminate things for sure and provide info for others to offer further assistance based on what you find.

Confirm you had a long and three short blinks?

Just got the airbox off and checked all the connections and it all looks good but same issue. I'll have to get a stethoscope and see if the injector is firing as the service manual suggests. (Downloaded a digital copy from the internet.) Then I'll do a continuity test for the injector plug and main connector to make sure I didn't damage one of the wires. But I never really put any stress on the injector connectors, just some of the other ones to get them through the routing.
Thanks very much for your prompt and useful replies!

FYI, was able to take the fuel rail off without removing the entire throttle body. Don't know why the book says to remove the throttle body to get the injectors off. It's ridiculous. Anyway, couldn't get the injector to work so I got 4 used ones on ebay for $85 instead of $156 for one new one from the dealer. TBC...

Oh no...I just switched injectors 1 and 2 around, not the connectors of course, just the injectors and got the same code "#13 which is #2 injector is bad.' Now I don't know where else to go???? Any ideas anybody.

Did you check continuity to the #2 injector from the main plug where the subharness connects to the rest of the wiring? I had a picture of which wire that was on my '04 in an earlier post when I dealt with the same issue. Maybe check continuity there and see if anything is amiss sending the signal to the #2 injector? Be sure to listen to the other injectors as well to compare what #2 sounds like; although I doubt you're getting a bad ECU code, it might help with the working/not working comparison on that specific injector vs ruling it out (I don't know what the sounding/stethescope would sound like to my untrained ear, so a comparison would be my only way of telling.)

Gus1300 First of all thanks for your replies!!!
I check continuity on the new sub-harness from #2 to the other end and it all checked out. THEN, I switched #2 injector with #1 injector and still got the same #13 code. That really scares me because what else could it be but the ECU? I checked all the wiring from the ECU to the front and clearly there is no further damage from those little SOB's. Today I'm going to switch some of the other injectors around just because I don't know what to do next and see what happens. I hate having a 700 lb boat anchor in my garage!

Hmmm...unfortunately that's about the limit of my troubleshooting skills from afar! Hopefully some of the other more experienced wrenchers on here can chime in with ideas; if you got no change from swapping injectors (and verified that neither injector functions when installed in the #2 position?) then it has to be the signal path to that position because it would rule out either injector being the suspected cause. Which would seemingly point to the ECU but I'm not sure there isn't something else between the ECU and the injector; still going with low likelihood of the ECU going bad because of a mouse nest under the airbox, only because of experience with the same situation and no affected ECU performance. Going to take a seat for a bit and watch what the real fixers can come up with. Good luck!

Well here it is, first I pulled the #2 plug which was brand new and it did not ever burn any fuel, still looked brand new. Checked to make sure it was sparking and it was. Just now I checked continuity all the way from the ECU plug to the #2 injector plug (same color wires all the way back) and they checked out, good continuity all the way back. Don't think it can be anything else but the ECU! So sad...

Anybody know where I can get an ECU/ECM? for a 2008 ST1300 NON-ABS? PLEASE give me a holler...

So my FI light is throwing a 26 blink code. Most references, and my manual, say that is a R. side knock sensor problem, BUT, I see some corrections that state the R. and L codes are reversed???. So I am asking, before I dive into this. is a 26 blink FI code R. or L. knock sensor problem? The bike is a 2003 ST1300A and I have a 2003 shop manual. Thanks to all.

Rickford said:

Sounds like you didn't pull the fuel rail either to replace the harness. I was worried that having to manipulate the harness to get it in place might have damaged it but getting the exact same code...I don't think so now. I'm going back in today and pull the tank and air box again and check it out. Guess I should have tried it before I put all that stuff on.

I should have mentioned that the bike was stored for about 2 years inside. But it was outside covered the last 5 months. I think that's when they (the mice) got me? But here's the other issue. During the two years it was stored It was filled with gas that had no stabilizer in it. At first I thought that bad gas was the problem and proceeded to remove all the fuel from the upper tank and finally worked down to the lower tank thinking maybe the filter was clogged. I pulled the cover from the lower and all that seemed fine, the filter was not clogged at all and the fuel pump was working fine since I could here it come up to pressure when I turned the key on. I also replaced the spark plugs. (During all of this I didn't know about the codes or how to get them, I came across that info from here.
Long story short, found the chewed wires, got a new harness installed and still get the same code: "#2 injector... I said all this not just to talk but to ask: Do you think that because the fuel was left in it so long that that injector is plugged up and thus not working? Just a guess. Also do you think the ECU got screwed up from the frayed wires? #1 and #2 injector wires were totally chewed and frayed all over the place.

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I just did this job and if you were to completely service the Tee properly yes remove the throttle bodies. To check connections and remove the tee even you can access without doing so. As pictured in the very center(with the 5 vac lines running to it lol). Getting down to throttle bodies is fairly simple looks intimidating but it's very straight forward. If you are entertaining the idea you likely have enough competence to figure it out to that point. Happy hunting. Replaced alt and had this after rebuilding loose connection on my 5 way throwing both a 2 and a 8 FI light.

Fortunet 1 said:

The "rough running" was only on a warm up cycle, but after cleared out it ran perfectly. One would think that the rough running would continue if a vacuum line was knocked off.?
Is that "five way tee" located behind the air box ? Just in front of the seat?

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The bike kind goes into a back up mode after a few seconds and then seems to run normally with a blocked vacuum T. It is not located behind the airbox but rather underneath it in the valley of the engine. You have to remove the entire airbox assembly to access it.

When you accessed the T it is not enough to inspect for any disconnections, you need to remove it and the 5 vacuum lined and blow or flush them all out. You can't tell if there's a blockage just by looking at them without removing and inspecting inside them. The typical issue is a blockage not a disconnection.