If it is the fuel pump or something like that, you should be able to pump the primer bulb and have it run well again. Usually when Yamaha pumps go bad, they idle poorly because gas goes into the crankcase. If you pump the bulb and it doesn’t help, I would revisit the carb, particularly the area between the fuel inlet nipple and the float valve.

If THE OWNER HIMSELF replaced the diaphragm, then, yeah, I would suspect he messed something up….

(You’re sure it’s not overheating, right?)