It sounds like the bike is heavy on fuel and looses power at higher speeds.
Before doing anything radical first check the carbs, one diaphragm might have a hole and you might as well replace the nozzle needles and the nozzle jets (needle jets) When these are worn they can cause a lack of power above 4000rpm. Something else to check is the nozzle needles position and, keeping in mind that it might need to be at a different position than the handbooks recommendation because the carbs is now used in a different configuration.
The smaller carbs will produce less power but will be better for fuel economy and will run smoother than the 40mm Bings. I have met some riders that sworn by this configuration so I would not change the carbs.
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