40mm Mikuni on SR500 single?

You've got a 7% increase in cylinder volume (535 vs 500) and are suggesting a 17% increase in fuel/air mixture for that volume. Did you re-jet the 34mm to compensate for the overbore? I think you'd be better served to find a tech with an EGA machine (exhaust gas yzer) and have your current carb re-worked rather than replace it with one designed for a 600cc motorcycle. You can make the bigger one work, but you need to consider changing to a free-flowing exhaust and changing cams to one with more lift or duration, depending on how and where you ride.