If it runs bad under a load it is either weak spark or poor gas flow.
Check all electrical plugs ( igniter box, etc.)
Replace the plug with an ngk b4.
Replace the gas filter or clean the main jet inside the carb if it runs better with the choke on.
Also check the fuel pump hose going to the engine crankcase and make sure there is NO gas in that hose. (pulses from engine drive pump)
make sure the engine is grounded to the control harness. (run a wire from the valve cover to the battery negative terminal. ( this works on all the yamahas that lose the ground to the engine)