Great, you are adventurous and may have gas in your veins!
Tips: make one change at a time, make changes big enough that they get your attention and adjust from there (bracket too rich, too lean, and then work to the middle), ride long enough with a change to understand its affects, pay very close attention to how the bike feels and responds, its safer to be a little rich than too lean. However, it is unlikely that you will burn the valves in a liquid cooled motor using 20% or less throttle so going too lean when cruising means a loss of power, surging, poor response to small throttle inputs, and reduced fuel mileage (but the engine will run cleaner to a point, hence OEM tuning that runs like sh-t.)
What can and often does happen when a little too lean is the engine will begin to ping (detonate.) As pinging increases, exhaust temperatures skyrocket. Early stages of detonation can't be heard with the human ear, so when you can hear it, it has already been occurring. Time to decide if you want to change timing or richen the mixture or perhaps both. Spark plugs can tell you a great deal about cylinder temperatures, detonation and combustion efficiency, but you have to know what to look for in general and then know what they look like in your engine which means the gas tank is up so often that you can remove the bolt and prop it up blind folded without scratching the tank.
Exhaust manifolds start to turn dull red at about 1,000 deg/F and is visible at night and progresses to orange by 1,300. In bright daylight you can't see dull red and may not be able to discern the early stages of orange that are readily visible at night (but an infared thermometer will.) Neither will damage your valves. Now if you see an orange glow in daylight or bright orange turning to yellow at night, well you might as well drive right to the garage as a valve inspection is in order. A side note here: a rich mixture, a relatively open or free flowing exhaust system, and late ignition timing makes for the nicest of blow torches. The exhaust system "lights" up from all the unburnt fuel combusting in the exhaust pipes, while the combustion chamber and cylinder head temperatures remain below normal. Quite a sight if one hasn't seen it before.
Too much fuel makes the throttle feel on/off or difficult to modulate; response to throttle input is immediate but sluggish. The engine may feel good if a little rich, but it won't be crisp. At larger throttle openings and faster acceleration rates, being rich is less noticeable but power is lost nonetheless. A disadvantage of having a fast bike to tune is that you have little time to sort out what you feel, as the speed changes so rapidly in lower gears and in higher gears your road speed becomes high enough that you become preoccupied with driving and have less ability to concentrate on what the engine is doing. Hence, sufficient riding time is needed to evaluate changes.
If you limit your tuning to low speed and cruising, you will discover that your senses are the best tools to use short of an eddy current dyno. Spark plug readings won't help much at very low speeds, but they are useful at cruising speeds (but you can't drive around town or stop and start the engine before checking them so carry tools with you, along with a pair of gloves.) Also, an old fashioned vacuum gauge used to determine engine load is helpful (or a computer strapped to the tank). Be aware that the R3 ECU has narrow limits within which to adjust the AFR. Although Tune ECU, for example, allows you to change the AFR table, the ECU won't compensate to those inputs if they are outside of its operating range. The stock O2 sensor is a narrow band design so that limits the range of adaptation (approx 14.05 to 14.70). You will discover that if you reset the adaptives and then ride the ECU will gradually adapt back to the range in which it can operate despite whatever numbers you have entered using TuneECU. The only way I could get my R3 to stay running correctly at low speed and cruising was to override the O2 sensor so that it wouldn't adapt at all.
Piggyback systems that use wide band O2 sensors can be set to richer or leaner AFR's than the stock system allows. Remember that no aftermarket company wants you to burn up your motor and then call them and complain about their "poor" product. So, their green, yellow and red indicators may be relative and useful but not necessarily definitive when applied to your application. Furthermore, they are limited in efficacy if they cannot change ignition timing. Spark timing and fueling are set by the OEM to reduce emissions and increase exhaust heat at idle and low speeds so that the catalytic converter lights off quickly and functions effectively in order to further reduce emissions to meet gov't requirements. Changing fueling only limits what can be accopmlished.
Enjoy the process and the potential outcome, but know there may be a little heartache along the way.
intake system type and size, fuel which varies from location to location, season to season, brand to brand, and in ethanol content; ignition system and controllers, which may or may not have detonation sensing ability and active compensation; operating conditions such as altitude, air temperature, and humidity; and operating mode as in half throttle to climb the Rockies at 80mph heading into a wind and pulling a trailer (sustained constant load and rpm) or half throttle while accelerating through the gears to reach 80mph (transient load and rpm.) And to make matters worse, sensors, injectors (or carburetor and components) and engines vary in manufacture and again over time with useage. Additionally, sensors have response times that affect their ability to capture "real time" data.
