I understand you meant no disrespect, and none was taken.
As I have said before, and I will probably say again, the CBR250 and Ninja250 are completely different in the way they will make power from modification. The Ninja already comes with a 12.5 to 1 compression ratio and a 12.5k redline. While it does lack some of the technological advancements (at least in stock USDM form) of the CBR, those two features alone allow the bike to put down more power in stock form.
Basically, the way the two bikes respond to tuning will be completely different. Tuning a CBR involves making advancements in power that were stock on the Ninja. Milling the head and/or installing a higher compression piston along with tuning the ECU to apply the appropriate amount of fuel for the higher compression ratio as well as raising the redline to 12.5k rpm puts the bike on equal footing technologically with the Ninja. Just a guess, but I would say that it would make similar power, likely in the high 20s low 30s range.
From this point, equal gains should be possible. Increase the size of the injector to match the CBR1000rr's injectors. Find aftermarket cams and adjust timing. Find a free flowing intake and exhaust, and install a slightly larger throttle-body. Tune accordingly. I would estimate a conservative 30-35bhp from all mods in total.
My initial 40bhp range may have been a bit out of reach, however, I see two examples why it is not entirely unreasonable.
The first is the production CBR1000rr, which shares the same bore, stroke, and valve diameter as the 250r's single cylinder. Conservatively, the 1000rr is making 160 hp, so naturally, one quarter of that would be 40 hp. I know there are other factors at play with a multi-cylinder engine, but it was a gross estimate.
The second example is the new Honda Moto3 race bike, the NSF250r, which features a single cylinder, four stroke, 250cc motor. The measured power on this bike is between 47 and 48 hp at 13k rpm. With a milder street tune, running on pump gas, 35-40 hp seems about right.
But lets be honest, anyone looking for a faster street bike isn't going to dump 5 grand into a 250 CBR or Ninja to make power, when they can sell the bike for 3k and take their 5k and buy a new 600cc or used liter-bike. Well, the only people I could see doing that are people who would want to use the bike for track days to learn on without buying a 600cc, and even then it would be easier to just step up to the bigger bike (I know I will, already eying the 675 Daytona), but it would still be interesting to see someone with a lot of disposable income take the CBR250 to its maximum performance capabilities.