I guess this goes back to what my Yamaha rep. said about switching out the pulley.
I've been working on cars since I was a kid, both at home and in dealerships, and I do agree with what you said..to a point. There are a lot of factors that go into the final injector signal. The most critical,and dynamic (and that everyone plays with) is the O2 sensor(s), the MAF sensor, and the IAT sensor. All the other ones are relatively static. The throttle position sensor tells the ECU "I am at position "a", therefore I need "
n" amount of fuel. Same with crank position, coolant temp sensor..etc. But the O2 sensor will hold reign over all the other ones, because that is the final one in the closed loop system. So regardless what the other sensors send to the ECU, if the O2 sensor thinks it's running too lean (or rich) it will tell the ECU to lengthen or shorten the injector pulse and the timing of the pulse. People either put a resistor in line with the IAT to which tells the ECU it's colder outside than it really is (and therefore the incoming air is denser) and needs to add fuel, or a resistor to the O2 which as everyone knows, tells the ECU it's running too lean and needs more fuel.
The tuners everyone puts on (myself included) compensate for larger amount of air coming through the intake. Stock ECU's can usually compensate satisfactorily up to a point. Aftermarket intakes and exhaust allow for more air intake/outflow, which "MAY" end up overwhelming the ECU, and cannot process a signal to compensate enough (depending on what you did, the stock ECU may be okay..you don't ALWAYS have to buy a tuner). All programming in an ECU is just a set of math functions, and if the results of the input do not fall within the criteria of a function set, the ECU will default to a parameter that will be less likely to hurt the engine (which is usually RUN RICH). The problem when this happens is premature fouling of plugs and O2 sensors due to excessive carbon build up...which then causes a crappy running engine in the long run (and if you have a catalytic converter, will also eventually plug it up).
So..my two cents for all the mod problems people have. Do your intake and exhaust mods first. If you have a significant problem compared to running stock, then spend the money on a tuner. When you unplug the O2 sensor or put in a resistor, you're making the engine run rich all the time, which is fine as long as you are aware of the long term effects as above. And when you do a mod...yes, you are changing what and how the bike was engineered to perform. So please do not ask for perfection from your mod.
It's like putting a radical camshaft in an engine, and then complaining because it doesn't idle nice....ain't gonna happen.
Sorry about the soapbox stance.