I'm still learning about these engines myself, but can offer a few things to consider.
1. Check the fuel plunger on the injection pump as it may be sticking a little. I've only seen these fully stuck and they have to be freed up. Since your engine is running at lower speeds, this could be a fuel metering issue.
2. If #1 doesn't apply, remove the valve cover to confirm valve lash and also verify both intake & exhaust valve are fully opening & closing.
3. If you haven't already done this, you should loosen the fuel line fitting on the injector and crank the engine over to confirm all air is bled from the line.
4. To confirm proper injector function (volume & spray pattern), you can remove the injector and reconnect to the high pressure fuel line (with the injector outside the engine). Then crank the engine over & observe injector function. (Caution: Don't get sprayed with the fuel mist!)
5. Check air filter and housing for any obstructions.
Edit: Forgot to mention that fuel injection timing is set by the thickness of the shim gasket(s) under the injector. If someone mixed these up, this could cause the plunger stroke to change, which would either advance or retard fuel delivery timing. Another remote possibility--the external throttle linkage is not correctly engaged to the injector metering linkage inside the engine. This can be seen by removing the small triangular inspection plate This plate covers a small "window" or port through which you can see the throttle linkage "bars" that should be engaged with the ball on the injection pump linkage. If the ball is not inside the two bars, this needs to be corrected.
A couple questions:
1. What type/color smoke are you seeing?
2. Any unusual noises when you start to throttle up? Backfiring, knocking??
I'm sure there may be other possibilities but wanted to offer a few that came to mind. Good luck with the troubleshooting!