It shouldn't have run at all without flap valves in the fuel pump - must have been stretching the pump diaphragm considerably to make it act like flaps. You will have to replace the diaphragm with the correct one of course - let's hope that fixes it, but there may have been damage to the piston and bore due to sustained running at full load with lean mixture.
The symptoms all along were a good match for fuel supply insufficiency, which is usually caused by intake fuel filter, fuel pump mesh screen, or fuel pump diaphragm, in pretty much that order of probability. Less likely, but sometimes happens, it could be low metering lever setting, crud in the passage from fuel pump to metering needle (only possible if it had been running without the screen on that passage), or sticking of a frayed viton section of the metering needle. At this point you seem to have dealt with most of that except for the intake fuel filter, as Joe pointed out. However, until you deal with the filter and replace the pump diaphragm, you probably won't know whether you've overheated the piston and ruined the engine. If you want to, you could remove the muffler and take a look at the side of the piston, through the exhaust port. If there is any scoring, or serious discolouring, there may be a problem. If it is smooth and shiny, you should be good to go when you finish fixing the fuel issue.