Is anyone running the ZX14 throttle bodies with the full Delkevic system?
Yes. Several people have because I have seen such postings in the past.
Does the flash cover any additional bottom end torque/hp loss?
That question doesn't relate to your first. I can answer in theory (which is supported by facts, like physics and dyno runs), and did so in my previous post. Yes, a reflash that is designed specifically for a "full exhaust" should be able to help some compared to a reflash not designed for a "full exhaust", but it will not recover all the lost low-end torque/hp. It is just a matter of physics
The Concours has more low-end power than a ZX-14 and less high-end power. Same displacement engine, different design parameters. Smaller exhaust/TB and different/variable cams allowed the Concours to be tuned to deliver more power in the "comfort" areas where "touring" users are more likely to use it and appreciate it. The opposite for the ZX-14, where the tuning (exhaust/TB different cam and lack of variable valves) shifted the power to the higher-end, raising the power (and, thus, maximum HP) in the range more appropriate for that type of rider.
The more the Concours engine setup is changed to be like the ZX14, the more loss of low-end power and the more gain in high-end power. It is a trade-off. Power can't be invented out of thin air- it is being shifted from one place to another.... aside from the fact that reflashing a stock Concours unlocks the full power it has because it undoes most of the things Kawasaki did for noise and emissions control (so that is kinda "free power").
Knowing the peak HP on a vehicle (which most people obsess over), which is a single point, doesn't tell the story of everything that came before it, as you can see in the attached graph. So.... is the ZX-14 (reflashed or not) more "powerful" than the reflashed (otherwise stock) Concours? No. Is it "faster"? In few cases, no. In most cases, yes. In some cases very much so. The ZX-14 is lighter (it has fewer features and storage and convenience), is more aerodynamic (making it more uncomfortable), is geared a little lower (which is better for getting the the higher RPM sooner, but not good for keeping in the comfort zone), and has a chain drive which reduces final drive loss (making it require more maintenance). The cam profile and lack of variable valves makes it less responsive and smooth, less fuel efficient, and louder, in the relaxed-riding RPM range. It also makes it, overall, less reliable. Trade-offs.