When you checked the fuel lines, did you look at the line inside the tank too? It doesn't take much, even a pin hole can cause issues. Also make sure that the cylinder head screws and back plate screws are tight?

You could also have something in the carb.

How did it run with the Pitts muffler at first? If it ran good, I doubt that could be a factor. Some people claim that they need to pinch off one muffler tube to build back pressure for good fuel flow. This has never been my experience though. then again, I've never tried a pitts on a .46-FXi.