Have you rechecked the lines inside the tank? Could there be a pinhole in the fuel line that sucks air when the tank gets low enough? Did the clunk get forced to the front of the tank?
Are you sure the fuel lines arent reversed like the carb is getting fuel from the vent line untill the fuel gets too low? I had an FP40 do this, never did figure it out, changed motors.

I think the FX 46 runs better with an APC 11x5 or 6 but as long as your rich enough the 11x4 shouldnt be a problem.