I have a 2002 CBR 954RR. It has a bad missing problem. I bought it around March 2009 and as far as I know it doesn't have any performance parts added except a Jardan exhaust. The 2 outside cylinders are the ones missing. But the thing is that it doesn't miss till it has been road a while. The distance traveled for it to start missing keeps getting shorter. I would say it started at bout 15 miles and its probly down to less than one mile before it starts to miss. It has good compression, good coils, its getting gas, its also getting spark. I have changed the spark plugs. I have also change the cam position sensor. I did replace it with a used cam position sensor but I would think that if it was bad too that it would have changed the problem in some way. I know its getting gas cause the unburned gas is coming out the exhaust big time and its getting spark cause while it was running it was taken apart to the point that we could unplug the coil and put a fresh spark plug n and it was sparking just fine. I had it a a honda dealer and they gave up after the cam position sensor and they suggested it might be the throttle bodies. But I really didn't want to put all that money in it and it not fix it.

 

Since your getting gas out the exhaust, I would lean towards the Fuel Pressure Regulator. If its messing up, it will let too much fuel pressure into the injectors and basically start to flood the engine out and you will get a surging/hesitation, just a really rich condition. Bad FPR's on early 2000 cbr's is quite common.

Hows your fuel mileage? If its on the low side, I would definately have the FPR checked.

 

Havent been able to even check the fuel milage. I don't know much bout a bike but I was tinkering with it some and found that there is a secondary method of putting fuel in the cylinder. And in turning the key on and holding the throttle open i noticed that there was gas pouring out of the other point of fuel source before hiting the start button. I am almost positive the cylinders are flooding im just not sure why. I don't know how the throttle body works with the secondary method of adding fuel. I was thinking it was only supposed to add fuel that way at higher rpms and that it is staying open.

 

The throttle body doesn't just push more fuel into the cylinders, its more complicated than that. Short description; it allows more AIR to flow into the cylinders. The bike responds by using output from its sensors to figure out how much fuel to push in.

I'd go with the pressure regulator first, then possibly the TPS (telling the bike its more open than it actually is), then maybe O2 sensor if you have one (telling the bike there's more oxygen in the exhaust than there actually is).