I'd double check your throttle cable, if it's not opening full throttle then the symptoms you describe could point to this.
I'm unfamiliar with your engine so it's difficult to suggest anything but the basics. If it's none of the above it does sound like it's a carb issue but I'd rule all the simple things out first before going down the carb blaming tearing your hair out route ; )
If it is a carb issue it sounds like it's an issue at low revs which would be down to the settings of the carb. The carb might need different settings if the new engine you have has different settings compared to your old engine.
Chris.
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