I am faced with the same thing.
I cleared out the complete fuel system & put a brand new carb on it. It did not help.
I now think it is the Reeds. The reeds are located where the carb connects to the engine. Reeds are simple intake valves, opening by vacume to allow air/fuel mixture into the engine. Reed valve engines deliver power over a wider RPM range.
They look and act like small playing cards in bike spokes, moving back & forth to open & close. They are made of a flexable materal, and when they get too soft with age & use, they don't open or close correctly.
"Delivering power over a wider RPM range" sounds exactly like what ours aren't doing! The reeds are on backorder at Yamaha, The whole assembly is $22. Just the reeds are $6. I ordered the whole assembly. I have not gotten them iet. They have some used ones on Ebay, but I want new. If you have other questions, I just bought the complete repair manual on CD.
boondawg@alaska.com
Boondawg, April 2008