Black box/fuel injection/flat spot

Have you checked that the fuel return line to the tank has not been crimped when the tank is lowered down as they changed these hoses in 01
(If I remember correctly) to a stiffer hose because of this problem,
If they line is crimped the fuel pressure in the system can be too high and cause rich running.

The 99s are prone to petrol filter problems and it is not unheard of the injectors getting partially blocked (especially the one closest tp the stand)
this will cause a poor spray pattern leading to fouling of the plug and poor running
 
All that is good to know but it still does not explain why the bike ran great for 3 months on the new ECU before starting to run like crap again.
And I was told the GSXR1000 and GSX1300R ECU were the same but I think the shop put in a busa ECU not hte GSXR's.
 
If you look at the boxws they are different in shape. and the box is the brain of the bike. It might have ran great for 3 months because it takes time for something to tear up. and theres really not that much difference in power between the two. I just don't think that was a good idea to put that box in its place.
 
I never said I put in a GSXR1000 ECU. I said I was told that they were both the same, the dealer said he ordered a ECU for the busa so I assume a busa ECU was installed. I have not had time to check the serial # of the unit that was installed and when I do I will post it. If it is a GSXR1000 unit I will be pissed and will pay that dealership a visit. I think that there is another problem burning out the ECU though.
 
I think a mulitmeter check in in order, at the fuse box, while the bike is off, turned on and ideling and at 5K rpm or so, just to be sure there isn't a voltage spike more than .75 V at any given time.
 
yea persuader I'd be pissed too. Take your bike to a dyno place. they can put your bike on the machine and tell you why its running like that. I had took my bike to a place like that and there were a # of things wrong things with my bike. And the mechanic told me about 3 months ago that my ECU was about to go out because it kept cutting off. It only would cut off when the bike was sitting still. And it would only do it every now and then.
 
Bro, tear you fuel pump apart and change out all of the little screens all over it. My 1999 did the same thing, so did my friends. Like ohzone said, the 99s are prone to fuel clogging problems. I changed my fuel filter quite frequently to solve this.
My was pretty clogged too at one point. Would loose power around 5-7k when I was going full throttle. When I punched it around that range to wheelie 2nd, it would hesitate pretty bad, jerk, lurch, then finally would take off. I bet you are suffering from fuel starvation just like I was.

As for your bike running good for 3 months, before I figured out my problem, it would run good for a while, then it wouldn't. It was sporatic and unpredictable just like yours sounds. iF they mapped it for more fuel, then yes, it would run better for a while, until the screens and filter got clogged even more. Make any sense?
 
How long did it take for your bike to start acting like that? Because I've had my bike for 2yrs now and got 12,000 mi on it.And I changed my filters and screens and it still runs bad. I even changed my #3 injector and it still skips.
 
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