Uh...why do you say I'm wrong....??
Having done electronic fuel injection calibrations for cars for many years (that drove good, passed the most stringent emissions standards, cold started at all ambients, etc...) I know a little bit about the systems and what it takes to cal them. Trust me, you are not going to get a total map done hitting all the various parameters in 2 hours on an inertia dyno.
Read my post again and explain to me exactly what you think is wrong. I'm simply curious.
I never said that the stock cal was "perfect" for driveability. It is obviously set up with emissions, driveability, engine durability, etc. in mind. It may not drive perfectly. Changing the part throttle air/fuel ratio may make it drive better. Doesn't mean it is making more power at part throttle necessarily. Especially if there were mods to the system the stock cal could be off in spots due to the mods. If an area of the stock map was a little lean, for instance, for emission purposes, then richening it slightly is going to "feel" good but you would never want to overly richen the part throttle operation to max torque for that particular throttle opening because the map would run rich all the time and fuel economy would suck.
I suspect the FJR is set a little on the lean side at idle and just off idle to help the oxidzing bed of the cat clean up HC and CO. This will feel a little stretchy and surgy on some engines. At any sort of load the system goes closed loop based on the O2 sensor input and the engine will run at 14.7:1 to make the cat work best for oxidizing HC and CO AND reducing NOx at the same time. It has to run at 14.7:1 to make a three way cat do this unless Yamaha has discovered something the rest of the world does not know about.
Many times less sopisticated fuel injection systems (like the FJR) will run a little lean on transients. That is, without an accelerator pump or accelerator pump "function" in the fuel injection pulse width computation logic a throttle opening maneuver will feel momentarily "saggy" or suggest a hesitation. Richening the map up in those areas will make it feel better for driveability but will then spike rich on throttle transisents hurting emissions. So the stock map is likely pretty accurate for steady state I'm guessing and the richening is helping the transient situation, not the steady state part throttle. Enabling the "accelerator pump" option on my PCIII helped the driveability without chaning the stock map at all.
So, sure, it is simple to add some fuel to the part throttle range and make the engine run more smoothly and possibly even get as good or even better fuel economy. But they are NOT tuning for best torque or power at part throttle points. That would make the whole map way too rich. Instead the cal is being pushed closer to 14.7:1 or 15:1 where driveability is very good and fuel economy is still OK.
Speed density systems like on the FJR can get really fouled up with anything that changes the tuning such as inlet mods or exhaust mods so a little detailed look at the map on a dyno is bound to help a little if mods have been made. It just isn't likely to be totally perfect as it is much easier to err on the rich side and have the good driveability.
Since the cal you mention was done in LV it cannot cover ALL the map anyway. Las Vegas is about 3000 feet in altitude I belive and the highest Barometer reading you are going to see there is 96 or 97 kPa if my memory is correct. Even at full throttle the most MAP the engine will see is 96 or 97 so there is no way they could run or replicate points on the fuel injection map above the mid 90's kPa. If you take your bike down to sea level and the baro is 103 (most liketly) then the engine MAP will be above what dynojet could run at LV. Hope they guessed good....LOL.
Really.....you're arguing with the wrong guy on this.....
BTW....I have a Holeshot header on my FJR also and have that same cal that was developed for your bike in my PCIII at the moment. It drives about like the cal I had developed from the seat of my pants and is actually pretty close in most areas numerically wise....even without a dyno..... The fact that mine drove the same with a slightly leaner cal also tells me that the holeshot cal developed there is a little on the rich side. See comments above.