Tuning is a complete mystery to me at this stage. I kinda get the principles but there's so much I don't get yet!
Whilst I do not know everything about tuning the principles are quiet simple.
The problem with modern engines is that the laws of emission, and noise are in direct conflict with the laws of tuning for best engine performance and longevity.
For an engine to pass emissions laws it has to run clean and quiet. Looking at the clean part first, ignoring the fresh air systems that draw in clean air to help fool the emission test, it means that we want the cleanest most efficient burn so that all the fuel is consumed and the minimum amount of nasty pollutants come out of the exhaust. The fuel ratio that achieves this is known as the stoichiometric air fuel ratio, which is about 15:1. 15 parts air 1 part fuel. Unfortunately, this clean burn also means a hot burn, and it also is not the best for power. The peak power is achieved around 14:1 or even lower 13.5:1. The extra fuel also cools the combustion chamber resulting in a cooler running engine.
As for the noise, restrictive exhausts and inlets are used to help keep the exhaust noise and inlet noise to a minimum, unfortunately this also means bad news for the engine, as it struggles to suck in fresh air. The less air we have, means the less fuel we can have, which means less power, then all the gases have to get out, and if they are restricted by a quiet exhaust, that means the engine can't get rid of the hot gases, which means again, less power and more heat.
So if we look at a stock engine, first off at cruise or slightly open throttle it is running in closed loop, which means the O2 sensors are dictating the AFR, which is set to run at stoichiometric for a clean burn to get through the emissions, which are tested at cruise, and slight acceleration. Only when you accelerate hard will the engine ECU look at the fuel tables and add fuel according to all it's other sensors, and run in open loop allowing a better fuel ratio. Most of the time its running in closed loop or lean.
Now add a free flowing air filter, and free flowing exhaust, and you have an engine that can breath, but requires more fuel. The fuel tables that the ECU uses for hard acceleration are not affected by the O2 sensor, so the ECU will continue to add only enough fuel for a standard engine, so it will run lean and hot.
The narrow band O2 sensors only work over a narrow AFR, and can't compensate for major changes in the state of an engine tune, so you'll run lean at cruise as well.
There are many options, including installing wide band O2 sensors as used with the Auto Tune devices, but from my experience and countless hours talking to tuners at raceways and tuning shops, the best way to tune an engine is on a dyno so you can remap the engine's ECU, or instal the industry standard tuning device which is the PCV.
The Harley system is great because you can just flash the ECU for whatever pipes and filter you have fitted.
I run a standard Voyager, with just an O2 eliminator, which means whenever the engine is in closed loop, looking for the O2 sensor to provide feedback on how the AFR is, the eliminator sets the AFR to 14:1 which is just enough to get rid of the rough running and flat spots, and keep things a little cooler. In fact, my main aim was a cooler running engine, and a set of slip on silencers and tuner from Cobra didn't keep the engine any cooler than just running the O2 eliminator with the rest standard, which tends to suggest the standard settings on the tuner were a bit off, giving another example of why you need to put your bike on a dyno to get it perfect. Dyno time isn't that expensive, certainly not as costly as a hole in you piston from running lean.
Hope this helps you understand a bit more, and for those that wish to pick holes in what I've said, yes, this is a
very simplified version because that's all I can cope with ha ha.