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This information has been gleaned from greg737, Somchai and various other information posted about EFI and the FI version Ninja 250R. This info will be updated as necessary.
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Basic Fuel Injection Information

Most factory EFI systems (cars and motorcycles) use one or more narrow-band O2 sensors, but these sensors aren't used in the manner you've described. These sensors are there mainly to confirm that the EFI system is functioning as it was designed to by the engineers. And on cars most of their concern is centered around emissions control.

In a factory EFI system the narrow-band O2 sensors are mainly there to confirm that the fueling is occurring correctly. If the system gets slightly off and the narrow-band O2 sensor reports crossing its 14.7 to 1 air/fuel ratio sweet spot at the wrong time the system is programmed to compensate a bit.

But if the narrow-band O2 sensor continually reports instances of "crossing 14.7" at weird or unexpected times compared to what the ECU is factory programmed for, as it would if you'd changed or modified the intake and exhaust, the EFI system will "throw a code" for maintenance and might even go into a "limp-home" mode.

An aftermarket EFI system like the Microsquirt ECU is purposefully set up for use with a wide-band O2 system so it can carry out "self tuning" operations on a do-it-yourself fuel injection system. A wide-band O2 system (the wide-band sensor plus a wide-band controller and a wide-band capable ECU) can read the whole spectrum of air/fuel ratios that an engine might experience during operation (while a narrow-band can only report when the air/fuel ratio crosses 14.7 to 1 air/fuel ratio).

You don't find wide-band O2 sensors on production vehicles because they cost quite a bit, they don't last nearly as long as narrow-band, and vehicle engineers don't need them anyway because they develop the car or motorcycle in a laboratory type environment in which they account for the engine's entire operating envelope ahead of time during testing.

They don't need or want to build in adaptability to allow people to change exhausts or intakes, where's the profit in that? There isn't any profit in that, which is why there's so many warnings about actions like that "voiding warranty". Messing with or changing the equipment, as installed at the factory, is bad for reliability which is the goal of a vehicle producer.

Having said all that, there's always an exception to every rule. There are aftermarket EFI systems that can do a pretty good amount of "auto tuning" activity. There's some tricky programming that can allow the ECU to predict and react to the small amount of information that a narrow-band sensor provides. The Ecotrons system does this.


Ninja 250R FI Tuning Information

You can tune the FI version Ninja 250R probably much easier than you can do to a carb-version, maybe not as cheap as though. Putting on a slip on exhaust should not require any other modifications of the Ninja’s FI system, neither should installing an aftermarket drop in type air filter.

If you are looking to improve performance and increase HP and choose to remove the air box, add a pod type filter and a full system, there are modifications that you must do.

The first thing to get is a good exhaust system, and it must be a full system. The Leo Vince Evo2 would be one of the best selections. (LeoVince Exhaust Systems have a new ECU for the EFI version 250 Ninjas. These units are installed in the 250 Ninjas for The WSBK European Junior Cup. Race-equipped Junior Cup Kawasaki Ninja 250R bikes are equipped with a full race exhaust and ECU.)

The second thing that is recommended is the LeoVince fast fuel-system ECU with the right mapping (http://www.leovince.com/en/catalog-k...008_2009/12087) with the full-system exhaust choose ref.# 8408 (works with or without air box modification and O2 Sensor). For this modification you need the O2-sensor removal plug. Removal of the O2 sensor is a MUST.

The other choice is the Power Commander V which comes with preset maps. Use of the PCV bypasses the O2 sensor which you need a plug (O2 eliminator) for.
http://www.power-commander-shop.com/...inja-250-R.htmt.

Disconnect the KLEEN air system (inlet air pressure) but don't disconnect the sensor because this will give you an error code in the FI-system. You only close/ block off the hoses.

As an option you can choose the Factory Pro ignition advancer. This will give you a 5 degree ignition advance, which may result in a 1-2 HP increase.

Remember
Dyno Tuning is highly recommended for any EFI System. A bike can run very strong after a mod, but actually may be running lean.
 
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