Larger injector, larger TB, ECU A/F tune.
You won't do much without pulling the head to be honest. The bike is a single cylinder that doesn't weigh very much. Pull the engine out (by hand with a friend) and pull the head, then disassemble the head and take it to a machine shop to have a thin slice machined off the mating surface with the cylinder sleeve/block. When you get it back from the machine-shop, take a dremel and (extremely slowly and carefully) match the ports for the intake and exhaust manifolds with the manifolds themselves and slowly open the runners into the head to match the opening that was just made (again, very slowly, you would rather do too little than too much). Clean the head thoroughly.
Next install Ti valves and stronger springs (if available, check the ones from a CBR1000rr as they should be extremely close) and some higher lift and duration cams. Also, if available, install adjustable cam timing gears. Set the timing after reassembling the engine with a tiny bit of overlap (exhaust stays open as the intake opens, drawing air in through a suction force).
Before reassembling the engine, take the time to buy new head bolts/studs, a new headgasket, and have the rings, bearings, and seals replaced as well as having the cylinder walls rehoned.
Reassemble everything and tune the A/F ratio accordingly to match the mods done. If possible, have the redline bumped to 12.5k rpm (or 13.5k rpm if you don't mind rebuilding the engine more frequently) to make the most of the top-end power that will be gained.
Make sure to have an open exhaust (no muffler or straight flow muffler with no catalytic converter), a free-flowing filter and intake assembly, a larger diameter throttle body, and a higher flow injector installed before tuning the ECU.
Break in the newly rebuilt engine, say goodbye to your Honda warranty, and enjoy your new, fast(er) CBR250r.
It would also be a smart idea to look at ways to improve the suspension (a la Racetech) and brakes (stainless lines or a dual front disc conversion off an older CBR250r model- the one that shares the front fork specifications as the new model).
Another way to speed up the bike is to drop weight, both from the rider and from the bike itself. The stock muffler and catalytic converter are heavy, around 20 lbs (or 8-9 kg if you prefer) and you will already be using a straight pipe so that weight will be gone. The tubing for your pipe could be replaced with Ti tubing shaving weight further. Loose the passenger footpegs and cover the rear brake fluid reservoir with a small piece of carbon fiber. Replace all body panels with carbon fiber if a replacement can be found (Tyga makes a good number). Replace parts with aluminum if a replacement can be found and the stock part is steel. Source an aluminum swing-arm and suspension components if replacements are possible (not sure if the stock pieces are steel, but the finish on them makes me suspect that to be the case. Loose the back seat in favor of a cowl made of CF (someone needs to come up with this ASAP). Replace the fairings with race bodywork if available, if not judiciously remove the inner plastic lining leaving a web pattern to drop some weight. And as a last resort, remove all body panel fasteners and hollow the shaft out with a drill press, leaving enough material to hold the panels in place without breaking. I estimate a drop of 30 lbs or more is possible from the bike. The rider, well, depends on how much you weigh now, and how much you want to work to lose weight, and if you empty your bowels before you ride. Your gear is another area, a lighter helmet and other gear (while still being protective) may cost a bit more, but if you are looking to cut weight, that is another area to look.
There are lots of ways to make the bike faster. However, the biggest question is, is the price worth the gain. Here in the states, I can sell the bike, take another 5000 USD and buy a brand new 600cc bike or a used literbike. The mods I mentioned would cost around the same price if not a bit more.
