FMS only adds fuel. The bike will adjust mixture based on altitude anyway. But the issue with these bikes, for EPA and mileage the mixture the ECU commands is very lean . So with pipes and more open air, you will NEED and FMS. So you did the right thing.
Here is a write up about this topic I did a while bike on another forum.
The ECU is the brain of the engine, it controls fuel, ignition, and monitors and has diagnostics. For now, let’s look at fuel and ignition.
Fuel maps are developed for all throttle positions, RPM, engine load, mixture setting requirements, air intake, etc. These maps are setup based on how the engine was intended to operate.
Ignition Timing is also controlled based on engine load RPM, throttle position and other variable.
The ECU is programmed based on requirements set buy the manufacture. With today’s EPA standards, the mapping is setup for emissions, and economy. Since motorcycles don’t have full blown emissions systems like cars. This makes the performance and readability undesirable. Also to make things worse, motorcycle ECU’s are limited on the real time adjustments they can make, so they cannot adjust adequately for modified intake and exhaust systems. This is where the tuners come in.
Tuners: Tuners were developed for 2 reasons, to try and smooth out the readability issues with stock ECU programming, and to enrichen the A/F ratio when adding air and exhaust. The simple tuners like Cobra and EJK (no maps) simply add fuel. The ECU normally sends a voltage to the injector to open it. This is typically called the injector pulse. Tuners are placed between the ECU ad injectors. When the ECU commands a “pulse” the Tuner tells the injector to stay open longer thus enriching the mixture. The tuner is simply increasing the injector pulse longer based on the ECU ratio. This helps immensely, but is not optimal because the tuners is simply following the ECU mapping but with a richer mixture. One big misconception: ECU units do not see the tuners or know they are even there. That is because with the fuel tuners, with O2 connections, the O2 connection on the tuner Lies to ECU into thinking that the lean mixture setting is still present. This prevents the ECU from trying to constantly lean the bike out when the tuners add fuel. That is why these tuners work better with O2 connections, to keep the ECU from trying to fix the richer setting.
Jacks O2 mod: Jacks O2 mod simply lies to the ECU and tells it that the mixture is too lean, the ECU responds and very slightly enriches the mixture, it helps but is far from optimal. But works for most who are on a budget. But this only works in the 500 to 4000 RPM range, which is where V Twins pretty much operate. But even though it is richer, it is still a lean mixture.
Ignition Timing directly effects power. Ignition timing refers to when the spark plugs are ignited. In engine 101 class we learn that the spark plug ignites the A/F mixture at the top of the compression stroke (TDC) top dead center. At very low RPMs it is acceptable to fire the spark plug fairly close to TDC. As RPM increases the piston actually is moving fast enough that it is running away from the combustion of the A/F mixture. This means when max cylinder pressure is achieved, the piston has already moved to the bottom of the travel therefore has nowhere else to go but up. This results in a loss of power. So as RPM is increased ignition timing is increased so the spark plug fires before TDC igniting the A/F mixture prior to TDC, of course this means the piston is working against the A/F combustion, but the fuel burn is not instant, it actually takes time. This means the piston still has a way to go down when max cylinder pressure is reached taking advantage of the pressure so that it is still pushing the piston down.
If the timing is advanced too much, this means max pressure will occur when the piston is fairly still high in travel meaning the area for combustion is small. This results in intense heat and then leads to the A/F mixture exploding (detonation), not burning. This results in high cylinder head and piston temperatures which results in engine damage. So there is a range of timing settings that are acceptable.
On our stock bikes the timing does advance as commanded by the ECU, but it is not advanced enough for power, instead it is a compromise to be delayed enough that the A/F mixture is still burning during the exhaust stroke, this is intended to keep the exhaust temps high to keep the catalyst converter hot so it works effectively.
So on our stock bikes, the A/F ratios, fuel mapping and ignition timing are not at all optimized for performance and ride-ability. Instead they are optimized for emissions.