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Discussion Starter #1 (Edited)
I have excerpted (and edited for clarity) a handful of things that stood out to me after @Dreadwil showed me this fine work Jesse from @Norton-Motorsports.com produced. Here's the original article. I've linked to all the parts Jesse referred to in the sections where they're appropriate.

I might add, reading his blog in the past (used to be YamahaR3Racing.com), inspired me to write the article on YZF-R3 and SpeedTek aRacer & AF1 or FT ECU, Bazzaz Z-AFM & Z-Fi ft. Full Exhaust Lists. Check it out. I'm no expert.

This experience changed my perception about tuning motors and my definition of “a good tune”. Instead of believing that a good tune is the one with the highest horsepower number on a chart, I now understand that it is more complicated than that. A good tune must take into consideration more info, like where the bike will be used, elevation, climate, fuel, and more importantly, how the bike performs when it’s slightly lean or slightly rich. A good tune is a balance of all of these factors to give as close to optimum performance as often as possible.
[With a full exhaust] you end up with a bike that runs WAY out of the ideal air/fuel ratio range...
...you are better off running the bike bone stock, or with a slip-on exhaust, than installing a full system exhaust without a fuel controller.
...I, and other tuners have seen over and over again, which is the fact that the R3 performs better with the noise restriction silencers installed in the exhaust, and always seems to be down on power with exhausts that are completely unrestricted in the end...[With the baffle-less] CRT version SC Project kinda falls on it’s face compared to the rest above 8000 RPM, even with a custom tune. This is the same thing we saw from the Yoshimura and Akrapovic stainless systems when the baffles were removed.
Akrapovic full system...was originally developed for the R25 in Asia...The original Akrapovic SS system had pretty dramatically smaller header pipes compared to some of the other systems, and was closer in size to the stock pipes.
Akrapovic reference

When the air/fuel ratio is properly adjusted using the Bazzaz Z-Fi, it performed exactly the same as the PCV with timing.
I also wanted to test the latest offering from SC Project, but unfortunately they sent me the CRT version, which is a pretty short, unrestricted (and very LOUD) exhaust.
I wonder if the "very short" had anything to do with the "very LOUD" on the SC Project CRT exhaust system.

[T]uning is different in each cylinder in a bike with staggered velocity stacks. Each cylinder requires different amounts of fuel at different times to match the resonance of air flow created by the different velocity stack lengths...modifying the airbox or velocity stacks to increase air flow means you will need to adjust fueling to match or you will likely lose power instead of gain.
Norton-Motorsports Velocity Stack reference

What I'm getting is that if I intend on leaving the airbox alone (I do), then going with the cheap R25 exhaust repackaged for the R3 might be just what I need; it won't open the exhaust enough to perhaps absolutely need airbox mods to compensate for the increase in exhaust flow. I'm not too excited about richening the AFR, as that just means less MPG. The problem with adding "performance mods" to the R3 is that most of them are designed for track use - which, as Jesse put it plain as day in the airbox mod section of his write up,

[O]n the race track, we don’t care so much about the area from idle to 9,000 rpm, and are much more concerned with the power above 9,000 rpm.

You can see that while changing the velocity stacks alone doesn’t have a huge effect on the peak HP number, it does change the power curve and drag the power band higher into the rev range, sacrificing some low end torque from 8,300-10,000 RPM, for top end horsepower above 11,000.
Much later in the article, he mentions Yamaha GYTR kit for racing (which includes two short velocity stacks), and tells all about the nasty performance deficits with two short stacks:

[Y]ou can see the nasty stair step in the midrange from Yamaha’s kit that’s result of running equal length stacks.
The chart he is referring to is here

I have NO interest in altering the internals of the R3 (too pricey for my interests), and airbox mods is definitely off the list.

Appreciable quote from The Man:

"Technology is awesome." - Jesse, @Norton-Motorsports.com

Jesse's writing is beautiful. His write ups are wordy, but he goes on to describe the problems with porting the head and realizing the throttle body was causing the bottleneck in airflow. I feel happy for Jesse on the work he's done and results he's realized through research & development (and is kind enough to share those results with us).

Norton-Motorsports Ported Head reference
Norton-Motorsports Ported Throttle Body reference

The paragraph on how fuel pumps work is coherent and actually entertaining; the reason you might hear the hum when Accessory-ON for the ignition is the fuel pump pressurizing the lines up to the fuel injectors. The fuel pump does this, because fuel injectors don't constantly feed, they pulse (for regular use). Jesse experienced (with ported heads and throttle bodies), "100% duty cycle"; the point at which his fuel injectors were constantly feeding fuel.

Norton-Motorsports Superbike Kit (includes modified Fuel Pump)

Delving into the section on ECU tuning, I came across the his testament of tuning the R3 using MAP instead of TPS, the aRacer standalone ECU.

The autotuner is also far more accurate than piggy-back autotuners and was the first one I felt could be trusted reasonably well when not used on a dyno.
This is Jesse's passion at work:

I ended up spending another 4 full nights (I’m talking like 6pm-4am long nights) and finally had a couple breakthroughs that opened up the capabilities of this tuning system.

The aRacer RC2’s ability to fine tune fueling through MAP pressure signal rather than TPS made a noticeable difference in performance and once I had it figured out, was so much easier to tune.
Norton-Motorposrts aRacer Super 2 reference
Norton-Motosports aRacer RCMini5 ECU (not referenced in the article)

Most "performance mods" are designed to open up the top end (track racing performance). This does NOT benefit street riders, as we operate (mostly for me, at least) in the low and mid range. To attest to this, here's another bit from his write up:

As for what’s the best exhaust, there’s some subjectivity in the answer, but I’ll be using the Graves Works 2 system on my bike and our team bikes for now.
Graves Works 2 simply isn't designed for the street. So that's leaves us back to the discussion regarding the Asia's R25 Chinesium (term coined by @Dreadwil) repackaged for the R3; it just might be what us street riders are asking for from a full exhaust, with tunable performance gains, subject to our own research & development for the streets.

Go to that discussion here.

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