Harley-Davidson Exhaust Replacement: Is it necessary to remap the fuel injection control unit?

This is one of the questions many fuel-injected motorcycle owners ask themselves, and curiously, the one that generates the most varied answers. I'll try to clarify the whys and hows, so you can draw your own conclusions with the right information.
Electronic fuel injection (EFI) has only recently become widely used in motorcycles, replacing the traditional carburetor. There are all sorts of opinions regarding this change, but it's a proven fact that fuel injection works much better, achieving more power, lower fuel consumption (and lower emissions), and greater smoothness than with a carburetor. It's as if we had the perfect carburetor, with hundreds of vents and circuits at the same time. Logically, as long as our fuel injection system is properly calibrated...
But what happens when we change the exhaust, air filter, camshaft, etc. on our motorcycle?

The engine runs on air!
Basically, what we're doing is varying the volume of air entering and exiting the engine. The engine runs on air, which is compressed and burned inside the combustion chamber to produce motion. More air means more power (which is one of the reasons why air filters and higher-flow exhausts are installed), but we mustn't forget that we combust that air by mixing it with gasoline. This is where our carburetor or EFI system comes into play. They're responsible for injecting the amount of gasoline necessary to combust the air entering the engine.
A carburetor performs this task by means of vacuum; if more air enters, the vacuum varies and, consequently, the amount of gasoline that enters, so in a way it self-compensates (this is only true to a certain extent, since generally the diffusers also have to be changed and "re-carburized" for everything to work perfectly).
In an EFI system, however, gasoline is injected under pressure directly into the intake manifold. The timing and quantity of gasoline injected are decided by the system's computer (or ECU, Electronic Control Unit). The amount of gasoline injected will depend on the information the system's sensors provide to the ECU (RPM, throttle opening, air temperature, atmospheric pressure, etc.). Based on this data, the ECU decides how much gasoline will be injected based on reference values programmed into tables (maps).
These programmed tables constitute the mapping of the injection system, and basically tell the ECU how much air is entering at a certain RPM and a certain throttle opening, and how much gasoline is to be injected.
If we change any component that affects this air intake or output (exhausts, filter, etc.), we must inform the ECU, that is, we must remap the injection. If we don't do this, the ECU will work with the correct values for our original exhausts and filters, which will lead to our engine running too lean on fuel. In the image, you can see how the mapping changes with a simple exhaust change.

If we add this problem to an engine that is already "lean" from the factory to comply with emissions regulations, we will have an engine overheating, and we will lose years of life... Regarding the "lean" or "rich" mixture, you simply have to know that the ideal mixture for perfect combustion is approximately 14.7 parts air to 1 part gasoline. A lean mixture generates excessive heat in the engine, and a rich mixture turns us into VIP customers at the gas station... In neither case will the bike run completely well, and we will not obtain the expected power and torque.

What does the escape have to do with all this?
Most people are quite clear that if we install an air filter that lets in more air, the mixture will become leaner, since we'll have more air for the same amount of gasoline.
What's less clear is why the exhaust can cause the same effect. To explain this simply, we need to talk about the waves produced when exhaust gases exit the exhaust pipe at high speed, creating a vacuum that generates waves that circulate toward the engine, in the opposite direction to the exhaust gases. When used correctly, these waves help improve cylinder filling at low and medium RPMs, where the motorcycle is most used. These pressure waves are technically known as backpressure or recoil waves.

If we change the exhaust to a more open one, these waves will vary, and consequently, the cylinder filling will increase, so the amount of fuel should also increase for the mixture to be adequate.
The injection control unit has no way of correcting these changes automatically, not even in models with an oxygen sensor or Lambda Probe (Dyna from 2006 and the rest of models from 2007 onwards), since the correction it can make is minimal.

Therefore, when we modify the exhaust or intake, we must rewrite the ECU's air tables (technically, Volumetric Efficiency tables). By doing so, we are informing the injection system of the actual amount of air entering and exiting the engine, and the ECU will adjust the fuel quantity accordingly. We will have a motorcycle that runs perfectly, without jerks, with good acceleration, and without excessive "backfires" when we take off the throttle. And, above all, our engine will run happier and cooler, something to keep in mind with a large-displacement, air-cooled engine.

So how do we do it?
There are several ways to rewrite or correct the Volumetric Efficiency (VE) tables or to increase the amount of fuel the system must inject. There are systems that intercept and modify the signal that the ECU sends to the injectors, simply by increasing the injector opening time. These systems can be programmed manually using potentiometers or buttons (Cobra Fi2000R, Arlen Ness Big Shot, etc.). An evolution of these devices are those programmed using software, where we can view the different tables and change the values (Dynojet Power Commander III, Daytona Twin Tec Tuner II, etc.). Some of these devices incorporate, as a novelty, a self-learning function, which means that they rewrite the tables themselves (Terry Components Terminal Velocity, Accel SLM, Power Commander V, etc.). Finally, we have the most sophisticated models, which write directly to the ECU's own tables and usually have self-learning and advanced functions (Dynojet Power Vision, Screamin' Eagle Super Tuner, Thundermax, TTS Mastertune, Fuelpak FP3 or FP4...).

In this other article, we discuss the differences between them and how to choose the right device and program it.

Conclusion:
By now, even if some of the concepts explained above still sound a little strange to you, you're probably pretty clear on the fact that it's absolutely necessary to work on the fuel injection system and remap it when changing any component that alters the amount of air entering or exiting the engine. From a simple exhaust and/or air filter change to displacement, camshaft, turbo, or intake manifold modifications, the fuel injection will always need to be modified—or, in other words, inform the ECU that new components have been installed—so that the bike runs smoothly, doesn't overheat, doesn't consume too much fuel, and accelerates like a true Milwaukee engine.