Yes, I have been told to that the KTM250 is the exact same EFI computer as the Husaberg models use.
I guess it could be anything. Have you gone through all the basic stuff?
Clogged Air Filter.
Clogged Muffler.
Spark Plug.
Still could be the injector. You might have got a piece of dirt in the fuel line when you put it back together after you cleaned it.
Has it got a decent Spark?
Or like CrazyTed says, it might just need a different EFI map loaded in, I have no idea.
Could also be a fuel pump issue which would be hard to check without a fuel pressure gauge.
Maybe Coil or Coil Lead at a long shot but I am guessing you would see some other issues other than just bogging down.
In "general" EFI term, the TPS (Throttle position sensor) is "usually" responsible for that instant Fuel Mixture enrichment at the exact time the throttle is opened quickly. The TPS sensor is mechanically connected to the Throttle Body Butterfly, which is directly connected to the Throttle cables, so it is the first sensor that knows the throttle has opened quickly. The TPS sends a signal to the EFI Computer that causes the EFI Computer to open the Fuel injector to let extra fuel in quickly and stop that bog down feeling. I am not sure if that is how it works in the EFI Keihin setup but that is how it works in some other EFI Computers. Having said the TPS does all that, you would think the EFI Light would flash 6 x Short Flashes to say you have a problem with the TPS Sensor or wiring.
Did you take it back to the dealer?
