Thanks for the information.
There are a few things I have seen cause this.
The first is to check that the correct 4 digit injector trim codes are programmed into the ECM. I have seen sometimes when they are wrong, it will cause the engine to run rough.
Second is a return line restriction. When there is a restriction it will cause the fuel in the head to get hit a aerate. This can cause the engine to run this way. I have seen injector o ring debris in the fitting on the back of the head, fuel line, and fuel pressure regulator.
Third is compression getting past an injector. To verify I like to install a clear sight glass on the fuel return line from the head. If it looks like beer foam. There compression getting past an injector.
Next is the parts department has given you the wrong injectors. I would double check and make sure they gave you the correct injectors.
Lastly is old software in the ECM. I have seen MBN engines with old software run like this.
Please reply back if you need more help or have more questions. I am happy to assist.