While I'm not exactly sure of what your problem is, a couple of things you might want to check are the fuel pump and all of the fuel line connections upstream of the pump.
It might be that the pump is not providing a smooth stream of fuel at those throttle settings where you are having trouble. If it is possible to run the pump while it is disconnected from the engine, do so and watch to see if the flow is smooth at all rpms.
Check all of the fuel connections for leaks, any leaks that are upstream of the pump will allow air to be sucked into the system, and will only get worse at higher throttle settings.
You did not mention which ECU you are using. The Sophia engines were sold with at least 3 different types of control systems and it would help to know which one you have.

Hopefully Marty Snell will chime in on this one, he has a lot of experience with Sophia's and might have more insight into what is going on.