Had a similiar problem on my bike recently.
Turns out to be a few small problems. First check you fuel lines to the engine, it sounds like it could be a restriction in fuel getting to the carbs, which would only be apparent at higher speeds when more fuel is needed. Make sure no kinks etc when the tank is in place. Also check the vacuum tube is in good condition, and again not kinked or so.
Sounds silly but it could also be the coils, or electrical system. My bike was running very badly accelerating to open road speeds, replaced a coil and problem was solved. Bike worked pretty much ok at lower speeds with the dodgy coil.
Stefan
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