Hello Rook!
I'm surprised that you aren't already.. since you did so much improvement or just maintenance to your bike - while making some very good manuals for the forum.. ;)
I had a Speed Triple, which had a free ECU flashing software (TuneECU) and OBD interface, so reading and writing was easy, and that ECU also had two AFR tables which made easy to make a tune that uses the O2 sensor data to keep the cruise (light load) lean but with liveable transition from that ECO but somewhat less responsible state to fully reactive to the throttle. And because of the OBD, I was able to log some values (rpm, AFR, etc) from rides, to see how my tune works in certain situations.
The Woolich software or even the Mitsubishi ECU seems to lack that tables, so it will need a different approach and/or it also needs some dyno tuning too if one aims peak torque/hp. On our own we have to lean on carb jetting symptoms and knowledge like that to see if the fueling around right. (for example it's leaner than should if we close the throttle on harder acceleration and it pulls for a moment before engine braking and that symptom exists on EFI engines too)
7k rpm: when the ZX14 arrived around 2006, I've seen a video that the secondary flies didn't even budged 'till 7000 RPM - and while I have the '08-11 version, it seems to behave like that, and 'till that RPM it pulls but I would say it pulls less than my former '07 ZX-10R, and also somewhat lagging fashion. Which still enough, but not that crispy, very throttle reactive way. So the bike feels too tame. (but also remember that around 2006 some drag race star said about the removed flies that it made the 14 so wild by the huge torque jump that it was spun the wheel or wanted to flip back at race start so it became uselessly wild)
Back to 7k: when a few times rolled the throttle and had the time (higway with guardrails and fence, so didn't had to watch the field for deers, etc) to watch the tach and the feel it is very noticeable how harder it accelerates - while on lesser bikes you know that above 220-240 km/h acceleration can start to taper off because air drag, and also this extra pull isn't the characteristic of an inline-4 which when it starts to pull it pulls somewhat linear fashion. So for me it seems obvious that's the secondaries work. - And if you watch Brock's series about the gixxer 1000 (or the zx10?) tuning to max on the dyno back from a few years ago, the factory made it's tune to close back the secondaries limiting the power output to around 150 HP, while the end result was around 200. On our bikes the secondaries use is more like to keep the brute force away.
What you say, to have the ECU flashed by a pro - or have the autotune kit is a smart way, but IMHO you shouldn't need to tweak then, only if you like to tinker. (read about Romans's, CBlast's and other flashes here how better they felt for most people who had them) I like to tinker and learn and sadly(?) I already ordered the basic kit (hopefully arrives next week), so will see by the results that I can figure it out (to make the on-off throttle transition, decel pop, etc. gone), or I'll look for a mail-in flash.
Thanks for stopping by, you're a "legend" for me in this forum :)