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Hope you get to ride soon. That will be the real test. Glad to hear it's firing on both cylinders now. NOW GO and RIDE

Spark, Fuel and Air... sometimes it is that simple. If the injectors aren't clean, the bike is starving for fuel.
HAPPY THANKSGIVING!
WhooooHooooooooo.... I dumped Gumout into the tank, it backfired, sputtered, and started. It ran on one cyclinder for about 30 seconds and then you could hear and feel the front cylinder trying to catch up. Within a minute it was only hitting and missing occasionally, and then it smoothed right out. I know you should not let your bike sit and idle for a long period but it was pretty decent out, not cold so I let it idle. Occasionally I would rev it a little to see what it would do, it never missed a beat,( smoked like a freight train though) remember I took the cobra commander off so it was running without it. After shutting it down and letting it cool I reinstalled the commander and fired it up again. Still running! Keeping my fingers crossed, it is supposed to rain here until Saturday so hopefully I will be able to take it on a trial run to burn that tank of gas out. Geezzz..we need to figure out how to get mechanics wages now 
The ECU is mounted next to the battery. Should be ok if the light functions as indicated in the tip.
You need to verify you are getting fuel to that cylinder. Injectors can foul and cause problems.
Hop it works.
The ride was great
suns a shining, which normally doesn't happen this time of year here in the Northwest.
Riding AGAIN!
Just funnin with ya! Have fun with that!
Okay, I will do the compression thing. thanks for the tip.
I am going to try the stp if you think there is a chance it could unplug the jet.
I hope you have another good ride. Mine is soon to come
(note my confidence!)
Easy way to check for compression, is move the spark plug wire out of the way (so you don't get a charge) hold your finger over the hole. press the starter switch until the cylinder makes a complete cycle,(unless you have a compression gauge). The compression should push the air around your finger, no matter how hard you hold it over the hole.
I too agree That DEALER mechanics are out to take your money. Private cycle shops want your business, so they don't try to take you for a ride.
Any jet cleaner will work. I use STP or gumout jet cleaner. Wally-world (Wal-Mart) sell them for about $2-3 abottle. use about 4-5 oz per tank.
If I remember right the ECU is the circuit board in the throttle body unit. I was told you can't replace just the circuit board. That's why It cost me $1000.00 for the new throttle body
WOW another nice day taking the black beauty out for another ride. Hoping yesterday wasn't a fluke, that it ran OK.
After printing off the self diagnosis I read it through. My FI light has not been on, it works but doesn't come on as a warning, so I don't think that is the problem, am I understanding that right? The self diagnosis is for checking when the FI light comes on?
1SG CAV- The mechanic didn't act like he was interested in working on a bike that had modifications done to it so he started talking about removing my new cobra part (because he didn't like that particular kind) he was going to charge me for a $400 for another brand that does the same thing. (go figure!) Then he said he would have to start all over and it would be around a grand by the time he was done. He is just guessing when it comes to the ECU, I think he is just figuring that since I have after market items on the bike that the ECU is no longer any good. I have one more referal to call. I have been told he is the best motorcycle mechanic around our area, he doesn't work for a dealer (I'm starting to think that is a plus) and he will come to my bike, I don't have to take it to him. I will wait until after this week to call. As far as the cylinder having good compression I don't know ( I'm a dummy in that area
) I wouldn't even know where to start. Is there a certain brand of jet cleaner I should use? I haven't ran any through it, and I am going to assume the previous owners didn't either. If I try that in my tank will it open a plugged jet?
You got to ride!!!!!!!!! awesome 
Did your last Mechanic tell you why you needed a new ECU? With fuel only going to one cylinder, the other has to be plugged. Have you every run jet cleaner in your tank? I run it with every other tank fill. If it is the jets then make sure you find a Good mechanic.
No rain today, got it running took mine for a 35 mile spin. still acts up, will be taking it in for tuning soon I hope.
does that cylinder have good compression?
Maybe the jet is plugged.
Anneoakley
I pulled my plugs today they were blacker than my bike. Cleaned them up, did a mild adjustment on the power commander. O got it running where I can ride it now. SO an advance tuning will/ should fix my problem.
With the power commander I can lean it out.
I have taken the Fi2000 off completely. No difference. Okay, I printed off the self-diagnosis. This will be all new territory for me....cool! I'll let you know what I come up with. Thanks Chief.
To run the bike needs, fuel, spark and air... if you are getting good spark, you need to start looking at the fuel system.
The FI2000 can be disconnected to eliminate it as a problem.
The question now is that cylinder getting fuel?Are you getting any error codes on the ECU?
Thanks, I put new plugs in did the check, got good spark from both, bike is still only running on one cylinder. (grrrrr) It is starting to look like I am running out of ideas.
pull the plug , then stick the plug wire on the plug, set it against the jugs so it is grounded, (do not hold it with your hands, unless you want YOUR battery charged)rubber handled pliers works. then turn the motor over look for spark. check with two different plugs,(one that you know works). If the good plug doesn't work then it's the wire, if it does then it's the plug.
Happy Hunting.
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